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home / skills / gptomics / bioskills
gptomics/bioskills
a set of SKILLS.md for doing bioinformatics with agents like claude code
421 skills
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grn-pipeline
gptomics/bioskills
262
This skill orchestrates a full gene regulatory network pipeline from single-cell data to regulon discovery and perturbation simulation.
ribosome-periodicity
gptomics/bioskills
262
This skill helps validate Ribo-seq data quality by checking 3-nucleotide periodicity and estimating P-site offsets for accurate downstream analysis.
msa-statistics
gptomics/bioskills
262
This skill computes MSA alignment statistics such as identity, conservation, and information content to evaluate alignment quality and evolutionary signals.
footprinting
gptomics/bioskills
262
This skill helps identify transcription factor footprints in ATAC-seq data using TOBIAS workflow to reveal TF occupancy patterns.
binding-site-annotation
gptomics/bioskills
262
This skill helps map CLIP-seq binding sites to transcript features such as 3'UTR, 5'UTR, CDS, introns, and ncRNAs in Python.
clip-peak-calling
gptomics/bioskills
262
This skill helps identify protein-RNA binding sites from CLIP-seq data by applying CLIPper, PureCLIP, or Piranha peak callers.
gatk-cnv
gptomics/bioskills
262
This skill guides CNV calling with GATK best practices, enabling somatic and germline CNV detection from WGS or WES data.
annotation-transfer
gptomics/bioskills
262
This skill transfers gene annotations to a new assembly using Liftoff and MiniProt, enabling fast, accurate annotations across species or assemblies.
targeted-analysis
gptomics/bioskills
262
This skill performs targeted metabolomics quantification from MRM data using calibrated curves, internal standards, and QC metrics to deliver accurate
tree-io
gptomics/bioskills
262
This skill reads, writes, and converts phylogenetic trees across Newick, Nexus, PhyloXML, and NeXML formats using Biopython.
fine-mapping
gptomics/bioskills
262
This skill helps you refine GWAS signals to likely causal variants by computing PIPs and credible sets using SuSiE and FINEMAP.
count-matrix-qc
gptomics/bioskills
262
This skill helps you assess RNA-seq count matrices for outliers, batch effects, and sample relationships to ensure robust differential expression results.
paired-end-fastq
gptomics/bioskills
262
This skill helps you manage paired-end FASTQ data with Biopython by synchronizing, filtering, interleaving, and auto-detecting R1/R2 pairs.
cnv-visualization
gptomics/bioskills
262
This skill helps you visualize copy number variation data across samples and produce publication-ready plots from CNVkit, GATK, or other callers.
preprocessing
gptomics/bioskills
262
This skill streamlines single-cell RNA-seq preprocessing by QC, filtering, normalization, HVG selection, and scaling in Python and R.
structure-modification
gptomics/bioskills
262
This skill enables programmatic protein structure modification using Biopython Bio.PDB, transforming coordinates, editing atoms or residues, and exporting
perturbation-simulation
gptomics/bioskills
262
This skill simulates transcription factor perturbations with CellOracle to predict cell state shifts and identify drivers of cell fate from TF knockouts.
positive-selection
gptomics/bioskills
262
This skill helps you detect positive selection in genes using dN/dS tests with PAML and HyPhy, identifying adaptive sites and branches.
bowtie2-alignment
gptomics/bioskills
262
This skill assists DNA read alignment with Bowtie2 in end-to-end or local modes, optimizing ChIP-seq and ATAC-seq workflows.
hisat2-alignment
gptomics/bioskills
262
This skill helps align RNA-seq reads using HISAT2, offering memory-efficient, splice-aware alignment for efficient gene expression workflows.
rmarkdown-reports
gptomics/bioskills
262
This skill helps you generate reproducible bioinformatics reports with R Markdown, rendering HTML, PDF, or Word outputs from parameterized analyses.
clip-pipeline
gptomics/bioskills
262
This skill guides end-to-end CLIP-seq analysis from FASTQ to binding sites and motifs, integrating QC, alignment, deduplication, peak calling, and motif
crispr-screen-pipeline
gptomics/bioskills
262
This skill orchestrates CRISPR screen analysis from FASTQ to hits, automating counting, QC, MAGeCK analysis, and multi-method hit calling.
longread-sv-pipeline
gptomics/bioskills
262
This skill guides end-to-end long-read SV analysis by aligning reads, calling SVs with sniffles or cuteSV, filtering, and annotating results.
somatic-variant-pipeline
gptomics/bioskills
262
This skill orchestrates a complete somatic variant calling workflow from tumor-normal samples using Mutect2 or Strelka2, including filtering and annotation.
spatial-proteomics
gptomics/bioskills
262
This skill analyzes spatial proteomics data from CODEX, IMC, and MIBI to phenotype cells, assess spatial neighborhoods, and integrate with transcriptomics.
model-curation
gptomics/bioskills
262
This skill guides you to validate, gap-fill, and curate genome-scale metabolic models using memote and COBRApy for publication-ready accuracy.
temporal-grn
gptomics/bioskills
262
This skill infers dynamic gene regulatory networks from bulk time-series data using Granger causality, dynGENIE3, and dynamic Bayesian networks to reveal
circos-plots
gptomics/bioskills
262
This skill helps you generate and customize circular genome visualizations using Circos and pyCircos, combining ideograms, genes, variants, CNVs, and arcs.
atac-peak-calling
gptomics/bioskills
262
This skill identifies open chromatin regions from ATAC-seq data by applying MACS3 with ATAC-specific parameters for expert peak calling.
interaction-databases
gptomics/bioskills
262
This skill queries STRING, BioGRID, IntAct and OmniPath to build protein interaction networks and retrieve confidence scores for analysis.
deseq2-basics
gptomics/bioskills
262
This skill guides you through performing differential expression analysis with DESeq2 in R, from dataset creation to shrunk fold changes.
clustering-phenotyping
gptomics/bioskills
262
This skill identifies cell types in high-dimensional cytometry using unsupervised clustering workflows like FlowSOM and Phenograph across samples.
assembly-qc
gptomics/bioskills
262
This skill assesses genome assembly quality by applying QUAST contiguity metrics and BUSCO completeness to guide assembler evaluation.
tumor-fraction-estimation
gptomics/bioskills
262
This skill estimates circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA, enabling tumor burden assessment and treatment
atlas-mapping
gptomics/bioskills
262
This skill maps single-cell data onto reference atlases using scArches, enabling label transfer with surgical fine-tuning and no retraining.
base-editing-design
gptomics/bioskills
262
This skill designs optimized base editing guides for cytosine and adenine edits, predicting outcomes to minimize bystander edits.
strain-tracking
gptomics/bioskills
262
This skill helps researchers track bacterial strains across samples by integrating MASH, sourmash, fastANI, and inStrain for outbreak and transmission analysis.
methylation-calling
gptomics/bioskills
262
This skill extracts per-cytosine methylation calls from Bismark BAM files and generates CpG, CHG, and CHH reports for downstream analysis.
mixomics-analysis
gptomics/bioskills
262
This skill helps you perform supervised and unsupervised multi-omics integration with mixOmics to identify discriminative feature signatures across groups.
haplotype-phasing
gptomics/bioskills
262
This skill helps you phase genotypes into haplotypes using Beagle or SHAPEIT for accurate downstream imputation and haplotype analysis.
modern-tree-inference
gptomics/bioskills
262
This skill helps you build publication-quality maximum likelihood phylogenetic trees from alignments using IQ-TREE2 or RAxML-ng with automated model selection.
star-alignment
gptomics/bioskills
262
This skill helps align RNA-seq reads with STAR in two-pass mode for improved splice-aware accuracy and downstream fusion detection.
peptide-identification
gptomics/bioskills
262
This skill identifies peptides from MS/MS spectra by database search, spectral matching, and FDR estimation using target-decoy approaches.
spectral-libraries
gptomics/bioskills
262
This skill helps you build, manage, and search spectral libraries for proteomics workflows, enabling DIA analysis with predicted and DDA-derived libraries.
cell-communication
gptomics/bioskills
262
This skill helps infer and compare cell-cell communication networks from scRNA-seq data using LIANA, CellChat, and NicheNet to identify ligand-receptor
trajectory-inference
gptomics/bioskills
262
This skill enables end-to-end inference of developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo.
adapter-trimming
gptomics/bioskills
262
This skill helps remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic to improve alignment readiness.
codon-usage
gptomics/bioskills
262
This skill analyzes codon usage, computes CAI, and examines synonymous bias using Biopython to aid expression optimization and evolutionary analysis.
trajectory-modeling
gptomics/bioskills
262
This skill fits smooth temporal trajectories to bulk omics time courses using GAMs, detects changepoints, and compares conditions to reveal dynamic differences.
volcano-customization
gptomics/bioskills
262
This skill helps you generate publication-ready volcano plots with customizable thresholds and gene labels using Python and R visualization libraries.
assembly-polishing
gptomics/bioskills
262
This skill helps you polish genome assemblies by applying Pilon, medaka, and racon workflows to improve base accuracy with short and long reads.
bed-file-basics
gptomics/bioskills
262
This skill helps you create, validate, and manipulate BED files across formats, enabling accurate genomic interval handling for downstream analysis.
fcs-handling
gptomics/bioskills
262
This skill helps you load, inspect, and manipulate Flow Cytometry Standard files in Python, enabling channel access, metadata retrieval, and basic exploration.
proteomics-qc
gptomics/bioskills
262
This skill helps you assess proteomics data quality by evaluating sample metrics, missing values, replicate correlations, batch effects, and intensity
hdr-template-design
gptomics/bioskills
262
This skill designs HDR donor templates for CRISPR knock-ins using primer3-py, creating ssODN, dsDNA, or plasmids with optimized homology arms.
fastq-quality
gptomics/bioskills
262
This skill helps you analyze and filter FASTQ reads by quality using Biopython, enabling trimming, reporting, and quality-aware filtering.
chipseq-visualization
gptomics/bioskills
262
This skill visualizes ChIP-seq data with heatmaps, profiles, and genome browser tracks to reveal enrichment patterns around peaks and TSS.
liquid-biopsy-pipeline
gptomics/bioskills
262
This skill helps you orchestrate a cfDNA liquid biopsy workflow from preprocessing to tumor fraction estimation and mutation detection, enabling end-to-end
multiome-pipeline
gptomics/bioskills
262
This skill guides end-to-end joint scRNA-seq and scATAC-seq analysis using Seurat and Signac, enabling WNN integration and multiome clustering.
tcr-pipeline
gptomics/bioskills
262
This skill guides end-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity, coordinating MiXCR, VDJtools, and Immcantation workflows.
structural-variants
gptomics/bioskills
262
This skill detects structural variants from long-read alignments using Sniffles, cuteSV, and SVIM, enabling accurate calls and breakpoint resolution.
clair3-variants
gptomics/bioskills
262
This skill runs Clair3 long-read variant calling for ONT or PacBio data, automating model selection and basic quality filtering to produce VCF outputs.
lipidomics
gptomics/bioskills
262
This skill helps analyze lipidomics data from LC-MS by identifying, quantifying lipids, and interpreting pathways with LipidSearch, MS-DIAL, LipidMaps.
functional-profiling
gptomics/bioskills
262
This skill profiles metagenomic functional potential using HUMAnN3 to produce pathway abundances and gene family counts for downstream analysis.
bismark-alignment
gptomics/bioskills
262
This skill aligns bisulfite sequencing reads using Bismark with Bowtie2 or HISAT2, producing BAM with methylation context.
methylkit-analysis
gptomics/bioskills
262
This skill analyzes DNA methylation with methylKit in R, importing Bismark data, filtering coverage, normalizing samples, and testing differential methylation.
structure-navigation
gptomics/bioskills
262
This skill helps you navigate Bio.PDB SMCRA hierarchy in Python to access structure elements, extract sequences, and inspect atomic coordinates.
methylation-pipeline
gptomics/bioskills
262
This skill guides end-to-end bisulfite sequencing analysis from FASTQ to DMRs, coordinating Bismark, methylation calling, and methylKit workflows for robust
similarity-searching
gptomics/bioskills
262
This skill finds and clusters chemically similar compounds using RDKit fingerprints and Tanimoto similarity to aid analog discovery.
substructure-search
gptomics/bioskills
262
This skill helps you identify compounds containing specific substructures in molecular libraries using SMARTS patterns with RDKit.
read-sequences
gptomics/bioskills
262
This skill helps you read and index biological sequence files efficiently with Biopython, enabling fast parsing, random access, and scalable workflows.
umi-processing
gptomics/bioskills
262
This skill helps you deduplicate reads using UMIs with umi_tools to enable accurate molecule counting in RNA-seq and single-cell workflows.
differential-analysis
gptomics/bioskills
262
This skill helps you perform differential abundance and state analyses on cytometry data to find condition-driven changes in cell populations and markers.
hic-pipeline
gptomics/bioskills
262
This skill guides end-to-end Hi-C analysis from reads to compartments and loops, enabling reproducible workflows and visualization.
expression-to-pathways
gptomics/bioskills
262
This skill guides you from differential expression results to functional enrichment across GO, KEGG, and Reactome with visualization.
figure-export
gptomics/bioskills
262
This skill exports publication-ready figures in PDF, SVG, and TIFF with correct resolution, sizing, and typography for journals and presentations.
data-import
gptomics/bioskills
262
This skill loads and parses mass spectrometry data formats (mzML, mzXML, MaxQuant outputs) with filtering and missing-value assessment to bootstrap analyses.
interactive-visualization
gptomics/bioskills
262
This skill helps you build interactive omics visualizations in Python using plotly and bokeh for exploration and web sharing.
alignment-io
gptomics/bioskills
262
This skill helps you read, write, and convert multiple sequence alignment files across formats using Bio.AlignIO for phylogenetics and conservation analysis.
pairwise-alignment
gptomics/bioskills
262
This skill performs pairwise sequence alignment using Biopython to compare two sequences, returning optimal alignments and scores for DNA, RNA, or proteins.
alignment-filtering
gptomics/bioskills
262
This skill filters BAM alignments by flags, MAPQ, and regions using samtools view and pysam to produce clean, targeted subsets.
alignment-indexing
gptomics/bioskills
262
This skill helps you enable random access to BAM/CRAM files by creating and using BAI/CSI indices with pysam and samtools.
alignment-sorting
gptomics/bioskills
262
This skill sorts alignment files by coordinate or read name using samtools and pysam to streamline BAM preparation.
alignment-validation
gptomics/bioskills
262
This skill validates alignment quality and post-alignment metrics to ensure reliable variant calling and quantification.
duplicate-handling
gptomics/bioskills
262
This skill helps you identify and remove PCR and optical duplicates in BAM files using fixmate and markdup to improve variant calling.
pileup-generation
gptomics/bioskills
262
This skill helps you generate pileup data for variant calling using samtools mpileup and pysam, enabling per-position analysis and allele frequency estimates.
differential-splicing
gptomics/bioskills
262
This skill detects differential alternative splicing between conditions using rMATS-turbo or SUPPA2 diffSplice, reporting FDR-significant events and delta PSI.
isoform-switching
gptomics/bioskills
262
This skill analyzes isoform switching with IsoformSwitchAnalyzeR to predict functional consequences and protein changes across conditions.
differential-accessibility
gptomics/bioskills
262
This skill helps you identify differential chromatin accessibility between conditions using DiffBind or DESeq2 in ATAC-seq experiments.
nucleosome-positioning
gptomics/bioskills
262
This skill helps identify nucleosome positions and occupancy from ATAC-seq data by integrating NucleoATAC, ATACseqQC, and fragment analysis.
bioskills-installer
gptomics/bioskills
262
This skill installs the full bioSkills collection to enable comprehensive bioinformatics analysis across 425 skills.
colocalization-analysis
gptomics/bioskills
262
This skill guides users through Bayesian colocalization to assess if GWAS and eQTL signals share a causal variant, with actionable interpretation.
mediation-analysis
gptomics/bioskills
262
This skill helps you perform causal mediation analysis on genetic data to decompose direct and indirect effects using molecular mediators.
molecular-descriptors
gptomics/bioskills
262
This skill computes molecular fingerprints and physicochemical descriptors with RDKit to enable ML featurization and screening of compound libraries.
molecular-io
gptomics/bioskills
262
This skill loads, standardizes, and converts molecular file formats using RDKit and Open Babel to prepare compounds for analysis.
virtual-screening
gptomics/bioskills
262
This skill enables structure-based virtual screening using AutoDock Vina by preparing receptors, generating ligands, docking, and ranking compounds by
chipseq-qc
gptomics/bioskills
262
This skill evaluates ChIP-seq data quality by computing FRiP, NSC/RSC, library complexity, and IDR concordance to guide downstream analysis.