Bioinformatics

Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU).

ClawBio/ClawBio

Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus…

ClawBio/ClawBio

Detect Neanderthal and Denisovan introgression segments from modern human genomes

ClawBio/ClawBio

Deterministic CRISPR screen hit ranking from local guide-level count tables

ClawBio/ClawBio

Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast outputs.

ClawBio/ClawBio

Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).

ClawBio/ClawBio

Score genetic compatibility across all male-female pairings in a Genomebook generation

ClawBio/ClawBio

End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing.

ClawBio/ClawBio

Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle.

ClawBio/ClawBio

Aggregates QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into a single MultiQC HTML report plus a ClawBio markdown summary with per-sample QC metrics.

ClawBio/ClawBio

Compute organ-specific biological age from Olink proteomic data using Goeminne et al.

ClawBio/ClawBio

Differential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and DIA-NN output.

ClawBio/ClawBio

Blood RNA-seq expression-outlier detection for rare-disease diagnostics.

ClawBio/ClawBio

Produce offspring genomes from parent pairs via meiotic recombination, mutation, and clinical evaluation

ClawBio/ClawBio

Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.

ClawBio/ClawBio

Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from…

ClawBio/ClawBio

NGS read QC, alignment, and BAM processing pipeline. An agent skill from ClawBio/ClawBio.

ClawBio/ClawBio

A skill your agent uses when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels…

xuzhougeng/wisp-science

Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes.

bioMate-AI/biomate-bioconductor-kb

UiPath automation genome (-genome.md): always invoke to build, execute or edit a genome file, before any skill it names.

UiPath/skills

Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap.

GPTomics/bioSkills

Comprehensive immune repertoire analysis for T-cell and B-cell receptor sequencing data.

wu-yc/LabClaw

Analyze spatial transcriptomics data to map gene expression in tissue architecture.

wu-yc/LabClaw

Run bioinformatics analyses using Lobster AI - single-cell RNA-seq, bulk RNA-seq, literature mining, dataset discovery, quality control, and visualization.

FreedomIntelligence/OpenClaw-Medical-Skills

Query GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative trait loci), and sQTLs.

LeonChaoX/qinyan-academic-skills

Candidate gene evidence from perturbation, dependency, resistance, sensitivity, viability, or assay-context records.

exon-research/genomi

Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.

wu-yc/LabClaw

Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics.

wu-yc/LabClaw

Production-ready RNA-seq differential expression analysis using PyDESeq2.

wu-yc/LabClaw

Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles.

wu-yc/LabClaw

Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE.

TianGzlab/OmicsClaw

Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.

ClawBio/ClawBio

Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.

ClawBio/ClawBio

Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination…

jaechang-hits/SciAgent-Skills

Parse and analyze multiple sequence alignments using Biopython.

GPTomics/bioSkills

Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner.

GPTomics/bioSkills

In recent years a wealth of biological data has become available in public data repositories.

bioMate-AI/biomate-bioconductor-kb

Stage 1 of the spatial transcriptomics workflow — load 10x Visium data and QC-filter low-quality spots.

QING1105/ezST

Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results.

aipoch/medical-research-skills

Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer.

GPTomics/bioSkills

Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero.

GPTomics/bioSkills

Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter.

GPTomics/bioSkills

Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter.

GPTomics/bioSkills

Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic.

GPTomics/bioSkills

Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW.

GPTomics/bioSkills

Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL +…

GPTomics/bioSkills

Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data.

GPTomics/bioSkills

Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data.

GPTomics/bioSkills