GPTomics/bioSkills.

bio-admet-prediction

Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts. Use when filtering compounds for drug-likeness or prioritizing leads by predicted safety.

bio-alignment-amplicon-clipping

Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.

bio-alignment-filtering

Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

bio-alignment-indexing

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.

bio-alignment-io

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

bio-alignment-msa-parsing

Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

bio-alignment-msa-statistics

Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.

bio-alignment-multiple

Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

bio-alignment-pairwise

Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.

bio-alignment-sorting

Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

bio-alignment-structural

Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

bio-alignment-trimming

Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

bio-alignment-validation

Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

bio-atac-seq-allele-specific-accessibility

Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

bio-atac-seq-atac-peak-calling

Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

bio-atac-seq-atac-qc

ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

bio-atac-seq-co-accessibility

Infer cis-regulatory connections (peak-to-peak co-accessibility) from scATAC-seq using Cicero, ArchR getCoAccessibility, or SCENIC+. Use when linking enhancer accessibility to promoter accessibility, identifying enhancer-gene pairs from chromatin alone (without paired RNA), running gene-regulatory inference combining ATAC + RNA, or comparing predicted regulatory contacts against Hi-C/Micro-C ground truth.

bio-atac-seq-consensus-peakset

Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

bio-atac-seq-deep-learning-atac

Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

bio-atac-seq-differential-accessibility

Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

bio-atac-seq-enhancer-gene-linking

Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

bio-atac-seq-footprinting

Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

bio-atac-seq-motif-deviation

Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

bio-atac-seq-nucleosome-positioning

Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

bio-atac-seq-single-cell-atac

Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

bio-bam-statistics

Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

bio-basecalling

Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses.

bio-batch-downloads

Download large datasets from NCBI efficiently using history server, batching, and rate limiting. Use when performing bulk sequence downloads, handling large query results, or production-scale data retrieval.

bio-batch-processing

Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.

bio-bedgraph-handling

Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq.

bio-blast-searches

Run remote BLAST searches against NCBI databases using Biopython Bio.Blast. Use when identifying unknown sequences, finding homologs, or searching for sequence similarity against NCBI's nr/nt databases.

bio-causal-genomics-colocalization-analysis

Test whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc. Computes posterior probabilities for shared vs distinct causal variants between GWAS and eQTL signals. Use when determining if a GWAS signal and an eQTL share the same causal variant.

bio-causal-genomics-fine-mapping

Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.

bio-causal-genomics-mediation-analysis

Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.

bio-causal-genomics-mendelian-randomization

Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when testing whether an exposure causally affects an outcome using genetic instruments.

bio-causal-genomics-pleiotropy-detection

Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instruments, or running sensitivity analyses for causal inference.

bio-cfdna-preprocessing

Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.

bio-chipseq-differential-binding

Identifies differentially bound ChIP-seq regions between conditions using DiffBind (from BAMs), DESeq2, or PyDESeq2 (from count matrices). Handles normalization, statistical testing, and fold-change estimation with ChIP-seq-specific considerations. Use when comparing ChIP-seq binding between experimental conditions.

bio-chipseq-motif-analysis

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.

bio-chipseq-peak-annotation

Annotate ChIP-seq peaks to genomic features and nearest genes. Classify peaks as promoter, exon, intron, or intergenic using ChIPseeker (R), HOMER annotatePeaks.pl (CLI), or Python (pandas/pyranges). Supports pre-built annotation databases and custom GTF files. Handles promoter definition, feature priority, category collapsing, and signed distance-to-TSS. Use when assigning genomic context to ChIP-seq peaks or linking peaks to target genes.

bio-chipseq-peak-calling

ChIP-seq peak calling using MACS3 and HOMER findPeaks. Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports single-caller and multi-caller consensus approaches, input control, fragment size modeling, and various output formats. Use when calling peaks from ChIP-seq alignments.

bio-chipseq-qc

ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.

bio-chipseq-super-enhancers

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.

bio-chipseq-visualization

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.

bio-clinical-biostatistics-categorical-tests

Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, and Cochran-Mantel-Haenszel tests. Computes effect sizes and post-hoc pairwise comparisons. Use when analyzing categorical outcomes or testing treatment-outcome independence in clinical trials.

bio-clinical-biostatistics-cdisc-data

Reads and prepares CDISC SDTM clinical trial data for analysis. Handles domain tables (DM, AE, EX, VS, LB), USUBJID-based joins, event-to-subject aggregation, and SUPPQUAL pivoting. Use when working with clinical trial datasets in CDISC/SDTM format or .xpt files.

bio-clinical-biostatistics-effect-measures

Computes and interprets treatment effect measures including odds ratios, risk ratios, number needed to treat, and confidence intervals from clinical trial data. Covers crude and adjusted measures, non-collapsibility of odds ratios, and forest plot visualization. Use when reporting treatment effects or comparing effect sizes across clinical studies.

bio-clinical-biostatistics-logistic-regression

Performs logistic regression for clinical trial outcomes including binary, ordinal, and multinomial models. Extracts odds ratios with confidence intervals, handles covariate adjustment, and provides Firth penalized regression for rare events or separation. Use when modeling binary or ordinal endpoints from clinical data.

bio-clinical-biostatistics-subgroup-analysis

Performs stratified and subgroup analyses for clinical trial data. Covers Mantel-Haenszel pooling, Breslow-Day homogeneity testing, interaction terms in regression, multiple comparisons correction, and forest plot visualization. Use when analyzing treatment effects across patient subgroups or controlling for stratification variables.

bio-clinical-biostatistics-trial-reporting

Prepares statistical tables and reports for clinical trials following regulatory standards. Generates Table 1 baseline characteristics, defines analysis populations (ITT, per-protocol, safety), performs multiple imputation for missing data, and follows CONSORT and ICH E9 guidelines. Use when creating analysis reports, handling missing data, or preparing regulatory submissions from clinical trials.

bio-clinical-databases-clinvar-lookup

Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.

bio-clinical-databases-dbsnp-queries

Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.

bio-clinical-databases-gnomad-frequencies

Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a variant is common in the general population.

bio-clinical-databases-hla-typing

Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.

bio-clinical-databases-myvariant-queries

Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.

bio-clinical-databases-pharmacogenomics

Query PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. Use when predicting drug response from genetic variants or implementing clinical pharmacogenomics.

bio-clinical-databases-polygenic-risk

Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.

bio-clinical-databases-somatic-signatures

Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.

bio-clinical-databases-tumor-mutational-burden

Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.

bio-clinical-databases-variant-prioritization

Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.

bio-clip-seq-binding-site-annotation

Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.

bio-clip-seq-clip-alignment

Align CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling.

bio-clip-seq-clip-motif-analysis

Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.

bio-clip-seq-clip-peak-calling

Call protein-RNA binding site peaks from CLIP-seq data using CLIPper, PureCLIP, or Piranha. Use when identifying RBP binding sites from aligned CLIP reads.

bio-clip-seq-clip-preprocessing

Preprocess CLIP-seq data including adapter trimming, UMI extraction, and PCR duplicate removal. Use when preparing raw CLIP, iCLIP, or eCLIP reads for peak calling.

bio-codon-usage

Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.

bio-comparative-genomics-ancestral-reconstruction

Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods. Infer ancient protein sequences and trace evolutionary trajectories through sequence history. Use when inferring ancestral states for protein resurrection or tracing evolutionary history.

bio-comparative-genomics-hgt-detection

Detect horizontal gene transfer events using HGTector, compositional analysis, and phylogenetic incongruence methods. Identify foreign genes in bacterial and archaeal genomes from anomalous composition or unexpected phylogenetic placement. Use when searching for horizontally transferred genes or analyzing genome evolution in prokaryotes.

bio-comparative-genomics-ortholog-inference

Infer orthologous gene groups across species using OrthoFinder and ProteinOrtho. Identify orthologs, paralogs, and co-orthologs for comparative genomics and functional annotation transfer. Use when identifying gene orthologs across species or building orthogroups for evolutionary analysis.

bio-comparative-genomics-positive-selection

Detect positive selection using dN/dS (omega) tests with PAML codeml and HyPhy. Identify sites and branches under adaptive evolution through codon models and branch-site tests. Use when testing for adaptive evolution in gene families or identifying positively selected sites.

bio-comparative-genomics-synteny-analysis

Analyze genome collinearity and syntenic blocks using MCScanX, SyRI, and JCVI for comparative genomics. Detect conserved gene order, chromosomal rearrangements, and whole-genome duplications. Use when comparing genome structure between species or identifying conserved genomic regions.

bio-compressed-files

Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.

bio-consensus-sequences

Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.

bio-copy-number-cnv-annotation

Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.

bio-copy-number-cnv-visualization

Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers. Use when creating genome-wide CNV plots, sample heatmaps, or chromosome-level visualizations.

bio-copy-number-cnvkit-analysis

Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use when detecting CNVs from WES or targeted panel sequencing data.

bio-copy-number-gatk-cnv

Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data. Use when following GATK best practices or integrating CNV calling with other GATK variant pipelines.

bio-crispr-screens-base-editing-analysis

Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies. Use when quantifying CRISPR base editor results, comparing ABE vs CBE efficiency, or assessing prime editing fidelity.

bio-crispr-screens-batch-correction

Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation.

bio-crispr-screens-crispresso-editing

CRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports. Use when analyzing amplicon sequencing data from CRISPR editing experiments to assess editing efficiency.

bio-crispr-screens-hit-calling

Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen count data after QC passes.

bio-crispr-screens-jacks-analysis

JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR screens simultaneously or when accounting for variable sgRNA efficiency across experiments.

bio-crispr-screens-library-design

CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designing custom sgRNA libraries for knockout, activation, or interference screens.

bio-crispr-screens-mageck-analysis

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis. Use when identifying essential genes, drug targets, or resistance mechanisms from dropout or enrichment screens.

bio-crispr-screens-screen-qc

Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery. Use when assessing screen quality before hit calling or diagnosing poor screen performance.

bio-ctdna-mutation-detection

Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor mutations from plasma DNA or tracking specific variants.

bio-data-visualization-circos-plots

Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs. Use when creating circular genome visualizations.

bio-data-visualization-color-palettes

Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes. Use when selecting colorblind-friendly palettes for figures.

bio-data-visualization-genome-browser-tracks

Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures. Use when creating publication figures of genomic regions with multiple data tracks.

bio-data-visualization-genome-tracks

Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV. Use when visualizing genomic data at specific loci with multiple aligned tracks.

bio-data-visualization-ggplot2-fundamentals

Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts. Use when creating static figures for papers, presentations, or reports in R.

bio-data-visualization-heatmaps-clustering

Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression and omics data visualization. Use when visualizing expression patterns across samples or identifying co-expressed gene clusters.

bio-data-visualization-interactive-visualization

Create interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations. Use when building zoomable, hoverable plots for data exploration or web dashboards.

bio-data-visualization-multipanel-figures

Combine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec with shared legends and panel labels. Use when combining multiple plots into publication figures.

bio-data-visualization-network-visualization

Visualize biological networks including gene regulatory networks, protein interaction networks, and co-expression modules using NetworkX, PyVis, and Cytoscape automation. Produces interactive and publication-quality network figures. Use when creating network diagrams from interaction data, GRN results, or co-expression modules.

bio-data-visualization-specialized-omics-plots

Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival curves. Use when creating volcano, MA, or enrichment plots.

bio-data-visualization-upset-plots

Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot. Use when comparing overlapping gene sets, peak sets, or sample groups with more than 3 sets.

bio-data-visualization-volcano-customization

Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib. Use when visualizing differential expression or association results with gene annotations.

bio-de-deseq2-basics

Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.

bio-de-edger-basics

Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.

bio-de-results

Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.

bio-de-visualization

Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.

bio-differential-expression-timeseries-de

Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns. Use when analyzing time-series or longitudinal expression data.

bio-differential-splicing

Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

bio-duplicate-handling

Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

bio-ecological-genomics-biodiversity-metrics

Calculates species richness, diversity, and turnover using the Hill number framework with iNEXT coverage-based rarefaction/extrapolation, asymptotic diversity estimation, and beta diversity partitioning (betapart turnover vs nestedness). Compares assemblages using coverage-standardized rather than size-standardized rarefaction. Use when quantifying biodiversity from species abundance or incidence data, comparing diversity across sites, or constructing rarefaction curves. Not for clinical 16S microbiome alpha/beta diversity (see microbiome/diversity-analysis).

bio-ecological-genomics-community-ecology

Analyzes community composition using constrained ordination (CCA, RDA, db-RDA), variance partitioning (varpart), indicator species analysis (indicspecies multipatt), and distance-based environmental gradient methods with vegan. Links species composition to environmental explanatory variables. Use when testing how environmental gradients structure species communities, identifying habitat indicator taxa, or partitioning explained variation among predictors. Not for basic unconstrained ordination and PERMANOVA (see microbiome/diversity-analysis).

bio-ecological-genomics-conservation-genetics

Assesses genetic health of populations for conservation using effective population size estimation (GONE2 for recent Ne trajectory, NeEstimator for contemporary Ne, Stairway Plot 2 and PSMC for historical Ne), F-statistics (hierfstat), runs of homozygosity (detectRUNS), and genetic diversity metrics. Use when estimating effective population size, detecting inbreeding or bottlenecks, or assessing genetic diversity in threatened species from microsatellite or SNP data.

bio-ecological-genomics-edna-metabarcoding

Processes environmental DNA metabarcoding data from raw amplicon reads to species occurrence tables using OBITools3, DADA2, and taxonomic assignment against BOLD, MIDORI2, or MitoFish databases. Handles COI, 12S, rbcL, and ITS barcode regions with primer removal, denoising, chimera detection, and contamination filtering via decontam. Includes occupancy modeling (occumb) for detection probability correction. Use when analyzing eDNA from water, soil, or bulk samples for biodiversity monitoring. Not for 16S human microbiome (see microbiome/amplicon-processing).

bio-ecological-genomics-landscape-genomics

Tests genotype-environment associations and identifies loci under local adaptation using LFMM2 (LEA), pcadapt outlier detection, OutFLANK Fst-based selection scans, and redundancy analysis. Detects adaptive genetic variation correlated with environmental variables while controlling for population structure. Use when identifying adaptive loci across environmental gradients, testing for signatures of local adaptation, or predicting genetic vulnerability to climate change with gradientForest.

bio-ecological-genomics-species-delimitation

Delimits species boundaries from molecular data using distance-based (ASAP), tree-based (bPTP, GMYC), and coalescent (BPP) methods. Compares multiple delimitation results with delimtools. Use when delineating putative species from DNA barcoding data, resolving cryptic species complexes, or validating taxonomic assignments. Emphasizes multi-method consensus following integrative taxonomy best practice.

bio-entrez-fetch

Retrieve records from NCBI databases using Biopython Bio.Entrez. Use when downloading sequences, fetching GenBank records, getting document summaries, or parsing NCBI data into Biopython objects.

bio-entrez-link

Find cross-references between NCBI databases using Biopython Bio.Entrez. Use when navigating from genes to proteins, sequences to publications, finding related records, or discovering database relationships.

bio-entrez-search

Search NCBI databases using Biopython Bio.Entrez. Use when finding records by keyword, building complex search queries, discovering database structure, or getting global query counts across databases.

bio-epidemiological-genomics-amr-surveillance

Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.

bio-epidemiological-genomics-pathogen-typing

Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.

bio-epidemiological-genomics-phylodynamics

Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states. Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees.

bio-epidemiological-genomics-transmission-inference

Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders.

bio-epidemiological-genomics-variant-surveillance

Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.

bio-epitranscriptomics-m6a-differential

Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states.

bio-epitranscriptomics-m6a-peak-calling

Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RNA immunoprecipitation data.

bio-epitranscriptomics-m6anet-analysis

Detect m6A modifications from Oxford Nanopore direct RNA sequencing using m6Anet. Use when analyzing epitranscriptomic modifications from long-read RNA data without immunoprecipitation.

bio-epitranscriptomics-merip-preprocessing

Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.

bio-epitranscriptomics-modification-visualization

Create metagene plots and browser tracks for RNA modification data. Use when visualizing m6A distribution patterns around genomic features like stop codons.

bio-experimental-design-batch-design

Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals.

bio-experimental-design-multiple-testing

Applies multiple testing correction methods including FDR, Bonferroni, and q-value for genomics data. Use when filtering differential expression results, setting significance thresholds, or choosing between correction methods for different study designs.

bio-experimental-design-power-analysis

Calculates statistical power and minimum sample sizes for RNA-seq, ATAC-seq, and other sequencing experiments. Use when planning experiments, determining how many replicates are needed, or assessing whether a study is adequately powered to detect expected effect sizes.

bio-experimental-design-sample-size

Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies. Use when budgeting experiments, writing grant proposals, or determining minimum replicates needed to achieve statistical significance for expected effect sizes.

bio-expression-matrix-counts-ingest

Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantification results for downstream analysis.

bio-expression-matrix-gene-id-mapping

Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources.

bio-expression-matrix-metadata-joins

Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.

bio-expression-matrix-normalization

Normalize and transform RNA-seq count matrices for differential expression, visualization, and clustering. Covers between-sample (TMM, RLE, upper quartile), within-sample (TPM, FPKM), variance-stabilizing (VST, rlog), and single-cell (scran) methods. Use when choosing or applying normalization to expression data.

bio-expression-matrix-sparse-handling

Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.

bio-fastq-quality

Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.

bio-filter-sequences

Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.

bio-flow-cytometry-bead-normalization

Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or harmonizing data across batches.

bio-flow-cytometry-clustering-phenotyping

Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.

bio-flow-cytometry-compensation-transformation

Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.

bio-flow-cytometry-cytometry-qc

Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying problematic samples before analysis.

bio-flow-cytometry-differential-analysis

Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.

bio-flow-cytometry-doublet-detection

Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering out cell aggregates before clustering or quantitative analysis.

bio-flow-cytometry-fcs-handling

Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.

bio-flow-cytometry-gating-analysis

Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifying cell populations through hierarchical gating strategies.

bio-format-conversion

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.

bio-fragment-analysis

Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection. Use when leveraging fragment patterns for tumor detection or tissue-of-origin analysis.

bio-gatk-variant-calling

Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.

bio-gene-regulatory-networks-coexpression-networks

Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes using WGCNA and CEMiTool. Detects hub genes and module-trait relationships from bulk or single-cell expression data. Use when finding co-expression modules, identifying hub genes, or relating gene networks to clinical or experimental variables.

bio-gene-regulatory-networks-differential-networks

Compare gene regulatory and co-expression networks between biological conditions to identify rewired regulatory relationships using DiffCorr. Detects gained, lost, and reversed gene-gene correlations between conditions. Use when comparing co-expression networks between disease vs control, treatment conditions, or developmental stages.

bio-gene-regulatory-networks-multiomics-grn

Build enhancer-driven gene regulatory networks by integrating single-cell RNA-seq and ATAC-seq data using SCENIC+ to identify eRegulons linking transcription factors to enhancers and target genes. Use when analyzing 10x multiome or paired scRNA+scATAC data to infer cis-regulatory GRNs.

bio-gene-regulatory-networks-perturbation-simulation

Simulate transcription factor perturbation effects on cell state using CellOracle, which integrates GRN inference with in silico knockout and overexpression modeling. Predicts cell identity shifts and differentiation trajectory changes from TF perturbations. Use when predicting the effect of transcription factor knockouts, planning perturbation experiments, or identifying driver TFs for cell fate transitions.

bio-gene-regulatory-networks-scenic-regulons

Infer gene regulatory networks and identify transcription factor regulons from single-cell RNA-seq data using pySCENIC. Discovers co-expression modules with GRNBoost2, prunes by cis-regulatory motif enrichment, and scores regulon activity per cell with AUCell. Use when identifying transcription factor regulons, scoring TF activity in single cells, or finding master regulators of cell identity.

bio-genome-annotation-annotation-transfer

Transfer gene annotations between genome assemblies using Liftoff for same-species annotation liftover and MiniProt for cross-species protein-to-genome alignment. Enables rapid annotation of new assemblies using existing reference annotations. Use when annotating a new assembly of a species with an existing reference annotation or mapping annotations across related species.

bio-genome-annotation-eukaryotic-gene-prediction

Predict protein-coding genes in eukaryotic genomes using BRAKER3 for combined RNA-seq and protein evidence, or GALBA for protein-only evidence. Runs Augustus with trained parameters for accurate gene models. Use when annotating a newly assembled eukaryotic genome or improving existing gene predictions.

bio-genome-annotation-functional-annotation

Assign GO terms, KEGG orthologs, Pfam domains, and EC numbers to predicted proteins using eggNOG-mapper and InterProScan. Produces functional summaries for downstream pathway and enrichment analysis. Use when adding functional annotation to predicted genes or characterizing protein functions in a new genome.

bio-genome-annotation-ncrna-annotation

Identify non-coding RNAs including tRNAs, rRNAs, snoRNAs, and regulatory RNAs using Infernal covariance model searches against Rfam and tRNAscan-SE for tRNA prediction. Use when performing genome-wide ncRNA annotation with assembly input producing GFF output.

bio-genome-annotation-prokaryotic-annotation

Annotate bacterial and archaeal genomes with Bakta for comprehensive structural and functional annotation, or Prokka for lightweight annotation. Generates GFF3, GenBank, and FASTA outputs with NCBI-compatible locus tags. Use when annotating a newly assembled prokaryotic genome or preparing annotations for NCBI submission.

bio-genome-annotation-repeat-annotation

Identify and classify repetitive elements and transposable elements using RepeatModeler for de novo repeat library construction and RepeatMasker for genome-wide repeat annotation. Quantify TE expression from RNA-seq with TEtranscripts. Use when masking repeats before gene prediction or analyzing transposable element activity.

bio-genome-assembly-assembly-polishing

Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.

bio-genome-assembly-assembly-qc

Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.

bio-genome-assembly-contamination-detection

Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies. Use when checking assemblies for contamination.

bio-genome-assembly-hifi-assembly

High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes.

bio-genome-assembly-long-read-assembly

De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions. Use when assembling genomes from ONT or PacBio reads.

bio-genome-assembly-metagenome-assembly

Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering metagenome-assembled genomes (MAGs), or resolving strain-level variation in complex samples.

bio-genome-assembly-scaffolding

Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps. Use when scaffolding contigs to chromosome-level assemblies.

bio-genome-assembly-short-read-assembly

De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes. Use when assembling genomes from Illumina reads.

bio-genome-engineering-base-editing-design

Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks. Use when designing base editor experiments for precise nucleotide changes.

bio-genome-engineering-grna-design

Design guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity using Rule Set 2 and Azimuth models. Use when designing sgRNAs for gene knockout, activation, or repression experiments.

bio-genome-engineering-hdr-template-design

Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms. Use when designing donor templates for precise insertions, tagging, or allele replacement.

bio-genome-engineering-off-target-prediction

Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity. Use when evaluating guide RNA specificity or selecting guides with minimal off-target risk.

bio-genome-engineering-prime-editing-design

Design pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks. Use when designing prime editing experiments for precise insertions, deletions, or point mutations.

bio-genome-intervals-bed-file-basics

BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools.

bio-genome-intervals-bigwig-tracks

Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions.

bio-genome-intervals-coverage-analysis

Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency.

bio-genome-intervals-gtf-gff-handling

Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or converting between annotation formats.

bio-genome-intervals-interval-arithmetic

Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools. Use when finding overlapping regions, removing overlaps, combining adjacent intervals, or transferring annotations between interval files.

bio-genome-intervals-proximity-operations

Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Use when performing TSS proximity analysis, assigning enhancers to genes, defining promoter regions, or finding nearby genomic features.

bio-geo-data

Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or linking GEO series to SRA runs.

bio-hi-c-analysis-compartment-analysis

Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices. Use when identifying A/B compartments from Hi-C data.

bio-hi-c-analysis-contact-pairs

Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.

bio-hi-c-analysis-hic-data-io

Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.

bio-hi-c-analysis-hic-differential

Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.

bio-hi-c-analysis-hic-visualization

Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.

bio-hi-c-analysis-loop-calling

Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts. Use when detecting chromatin loops from Hi-C data.

bio-hi-c-analysis-matrix-operations

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.

bio-hi-c-analysis-tad-detection

Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores.

bio-imaging-mass-cytometry-cell-segmentation

Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation. Use when extracting single-cell data from IMC or MIBI images after preprocessing.

bio-imaging-mass-cytometry-data-preprocessing

Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.

bio-imaging-mass-cytometry-interactive-annotation

Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training classifiers or validating automated phenotyping results.

bio-imaging-mass-cytometry-phenotyping

Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.

bio-imaging-mass-cytometry-quality-metrics

Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality before analysis or troubleshooting problematic acquisitions.

bio-imaging-mass-cytometry-spatial-analysis

Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when analyzing spatial relationships between cell types, testing for neighborhood enrichment, or identifying cell-cell interaction patterns in imaging mass cytometry data.

bio-immunoinformatics-epitope-prediction

Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens. Use when designing vaccines, mapping antibody binding sites, or predicting immunogenic peptides.

bio-immunoinformatics-immunogenicity-scoring

Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design. Use when prioritizing epitopes for vaccine development or identifying the most immunogenic neoantigens.

bio-immunoinformatics-mhc-binding-prediction

Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences. Use when predicting MHC binding for vaccine design or neoantigen identification.

bio-immunoinformatics-neoantigen-prediction

Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient HLA and may elicit T-cell responses. Use when identifying vaccine targets or checkpoint inhibitor response biomarkers from tumor sequencing data.

bio-immunoinformatics-tcr-epitope-binding

Predict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition. Match TCRs to their cognate epitopes or predict TCR targets. Use when analyzing TCR repertoire specificity or identifying antigen-reactive T-cells.

bio-interaction-databases

Query protein-protein and gene interaction databases including STRING, BioGRID, and IntAct via their REST APIs and Python clients. Retrieve interaction networks, confidence scores, and functional enrichment. Use when building protein interaction networks, contextualizing gene lists with known interactions, or retrieving pathway-level interaction data.

bio-isoform-switching

Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

bio-liquid-biopsy-pipeline

Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy samples for cancer detection or monitoring.

bio-local-blast

Run local BLAST searches using BLAST+ command-line tools. Use when running fast unlimited searches, building custom databases, performing large-scale analysis, or when NCBI servers are slow or unavailable.