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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.

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gptomics/bioskills

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