Bioinformatics

Analyze transcription factor motif accessibility variability using chromVAR.

FreedomIntelligence/OpenClaw-Medical-Skills

Differential binding analysis using DiffBind. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP.

FreedomIntelligence/OpenClaw-Medical-Skills

Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker.

FreedomIntelligence/OpenClaw-Medical-Skills

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

FreedomIntelligence/OpenClaw-Medical-Skills

Visualize copy number profiles, segments, and compare across samples.

FreedomIntelligence/OpenClaw-Medical-Skills

Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies.

FreedomIntelligence/OpenClaw-Medical-Skills

Batch effect correction for CRISPR screens. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

CRISPResso2 for analyzing CRISPR gene editing outcomes. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality.

FreedomIntelligence/OpenClaw-Medical-Skills

CRISPR library design for genetic screens. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Statistical testing for differentially abundant proteins between conditions.

FreedomIntelligence/OpenClaw-Medical-Skills

Quick-reference sheet for OmicVerse tutorials spanning MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.

FreedomIntelligence/OpenClaw-Medical-Skills

Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees.

jaechang-hits/SciAgent-Skills

Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic…

jaechang-hits/SciAgent-Skills

Cancer genomics (TCGA et al.) via cBioPortal REST API. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

JASPAR 2024 TF binding profiles via REST API and pyJASPAR. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Build, read, validate, modify SBML biological network models via the libSBML Python API.

jaechang-hits/SciAgent-Skills

Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology.

jaechang-hits/SciAgent-Skills

Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API.

jaechang-hits/SciAgent-Skills

Query EBI QuickGO REST API for GO terms and protein annotations.

jaechang-hits/SciAgent-Skills

Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state).

jaechang-hits/SciAgent-Skills

Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies.

jaechang-hits/SciAgent-Skills

Predict RNA secondary structure, MFE folding, base-pair probabilities, RNA-RNA interactions via ViennaRNA Python bindings.

jaechang-hits/SciAgent-Skills

BUSseq R package fits an interpretable Bayesian hierarchical model---the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)---to correct batch effects in the presence of…

bioMate-AI/biomate-bioconductor-kb

A skill your agent uses whenever the user wants reproducible CS/AI experiments, model evaluation, regression/classification/clustering analyses, bioinformatics workflows, QC, differential…

Citrus-bit/Anaxa

Load when placing bulk RNA-seq samples on a single-cell reference's pseudotime axis (NNLS deconvolution + nearest-neighbour mapping).

TianGzlab/OmicsClaw

Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2…

TianGzlab/OmicsClaw

Load when computing genome-assembly QC metrics — N50/N90, L50/L90, total length, contig count, GC content, longest-contig — from a FASTA produced by any assembler (SPAdes / Megahit / Flye / Canu).

TianGzlab/OmicsClaw

Load when calling CNV segments via CBS-style segmentation on a bin-level log2-ratio CSV from exome / WGS coverage — emits per-segment 5-class CN state (amplification / gain / neutral / loss /…

TianGzlab/OmicsClaw

Load when summarising a peak file (BED / narrowPeak) from ATAC-seq / ChIP-seq / CUT&Tag — peak count, width distribution, per-chromosome counts, score statistics.

TianGzlab/OmicsClaw

Load when summarising a phased VCF (output of WhatsHap / SHAPEIT5 / Eagle2) — phased fraction of het variants, phase-block N50, PS-field parsing, pipe-delimited genotype detection.

TianGzlab/OmicsClaw

Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection.

TianGzlab/OmicsClaw

Load when summarising structural variants from an SV VCF (DEL / DUP / INV / TRA) — INFO/SVTYPE-based classification, size classification, per-type counts.

TianGzlab/OmicsClaw

Load when summarising functional impact of an annotated variant CSV — per-IMPACT counts (HIGH / MODERATE / LOW / MODIFIER), top consequences, gene-affected count.

TianGzlab/OmicsClaw

Load when summarising small variants (SNVs / indels) from a VCF or computing demo-pattern variant statistics (Ti/Tv ratio, per-chromosome distribution, SNP / indel split).

TianGzlab/OmicsClaw

Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing.

TianGzlab/OmicsClaw

Load when ingesting a MaxQuant proteinGroups.txt, FragPipe combinedprotein.tsv, DIA-NN report, or generic CSV / TSV protein-quantification table — normalises columns to a standard schema, emits…

TianGzlab/OmicsClaw

Load when computing two-group differential protein abundance (group2 vs group1, log2FC + p-value + BH-adjusted FDR) via Welch t-test, equal-variance t-test, or Mann-Whitney on a wide protein ×…

TianGzlab/OmicsClaw

Load for Fisher over-representation analysis of protein identifiers against caller-supplied pathways.

TianGzlab/OmicsClaw

Load when summarising peptide identifications (PSM count, unique peptide count, distinct protein count, score / charge distributions) from a peptide-level CSV produced by MaxQuant / FragPipe / DIA-NN.

TianGzlab/OmicsClaw

Load when computing protein-table QC — proteins × samples count, missing-value rate, intensity CV (median + mean) — from a MaxQuant / FragPipe / DIA-NN protein-quantification CSV.

TianGzlab/OmicsClaw

Load when summarising PTM sites (phosphorylation, acetylation, ubiquitination, etc.) from a per-site CSV — site-class assignment (Olsen et al.

TianGzlab/OmicsClaw

Load when computing per-protein abundance from a peptide / PSM table via LFQ (intensity summation), iBAQ (intensity / tryptic peptide count), or spectral counting (PSMs per protein).

TianGzlab/OmicsClaw

Load when summarising cross-linking MS (XL-MS) results — intra/inter-protein link split, optional FDR filtering, distance-constraint validation against a per-crosslinker (DSS / BS3 / EDC / DSSO /…

TianGzlab/OmicsClaw

Load when removing ambient RNA contamination from droplet-based scRNA-seq using a simple subtraction path, CellBender, or SoupX.

TianGzlab/OmicsClaw

Load when integrating multi-sample scRNA-seq with Harmony, scVI, scANVI, BBKNN, Scanorama, SIMBA, or supported R-backed methods to remove batch effects.

TianGzlab/OmicsClaw

Load when assigning cell-type labels to a clustered scRNA AnnData via marker dictionaries, CellTypist, PopV, KNNPredict, SingleR, scmap, SCSA, or a manual cluster-to-label map.

TianGzlab/OmicsClaw