Media & Creative · Bioinformatics

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.

google-deepmind/science-skills

Fetch Evolutionary Conservation scores (phyloP, phastCons) and Transcription Factor Binding Sites (TFBS) from the UCSC Genome Browser.

google-deepmind/science-skills

Infers candidate gene regulatory networks from bulk or single-cell expression data using AertsLab Arboreto GRNBoost2 and GENIE3.

K-Dense-AI/scientific-agent-skills

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

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

Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing.

GPTomics/bioSkills

Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs).

LeonChaoX/qinyan-academic-skills

Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity…

GPTomics/bioSkills

Simulate transcription factor perturbation effects on cell state in silico with CellOracle and Dynamo, and predict transcriptional responses to genetic perturbations with GEARS, scGen, and CPA.

GPTomics/bioSkills

Designs pegRNAs and nicking guides for prime editing (PE) -- choosing the nick/strand, tuning the primer-binding site (PBS) and reverse-transcription template (RTT) as a per-locus panel, selecting…

GPTomics/bioSkills

Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython and regex, including position weight matrix (PWM/PSSM) scoring.

GPTomics/bioSkills

Transcribe DNA to RNA and translate to protein using Biopython, with NCBI codon-table selection, CDS validation, and six-frame ORF finding.

GPTomics/bioSkills

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools…

GPTomics/bioSkills

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools.

FreedomIntelligence/OpenClaw-Medical-Skills

Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS.

FreedomIntelligence/OpenClaw-Medical-Skills

Analyze transcription factor motif accessibility variability using chromVAR.

FreedomIntelligence/OpenClaw-Medical-Skills

ChIP-seq peak calling using MACS3 (or MACS2). An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Load when computing cell-cell ligand-receptor communication on an annotated scRNA AnnData via builtin scorer, LIANA, CellPhoneDB, CellChat (R), or NicheNet (R).

TianGzlab/OmicsClaw

This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype.

bioMate-AI/biomate-bioconductor-kb