Bioinformatics

Query the Ensembl database to resolve gene, transcript, and protein IDs, fetch genomic or protein sequences, retrieve gene structures (exons), and get variant consequence and effect predictions (VEP).

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

Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.

ClawBio/ClawBio

A skill your agent uses when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery.

ynulihao/AgentSkillOS

Evaluate and use SSH Remote Compute before choosing where to run GPU, high-memory, parallel, batch, model-inference, bioinformatics, or other long-running scientific work; supports short remote…

aipoch/open-science

This package provides a client for the Bioconductor AnnotationHub web resource.

bioMate-AI/biomate-bioconductor-kb

Access NCBI GEO for gene expression/genomics data. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Plan, validate, and document public-bioinformatics data acquisition for GEO/GSE/GSM/GPL/GDS, SRA/ENA, TCGA/GDC, GTEx, and DepMap.

xuzhougeng/wisp-science

Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources.

exon-research/genomi

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam.

GPTomics/bioSkills

7-section readiness scorecard for a LOCAL repo. An agent skill from ruvnet/metaharness.

ruvnet/metaharness

Extract TCR:pMHC specificity records from raw submission sources - supplementary XLS/CSV tables, PDF manuscripts, 10x Genomics contig and clonotype files, AIRR Rearrangement TSVs, Adaptive ImmunoSEQ…

antigenomics/vdjdb-db

Atera platform branch of the spatial transcriptomics workflow — load and validate Atera cell-level output (AnnData + Zarr segmentation) for downstream analysis.

QING1105/ezST

Load when discovering bulk gene co-expression modules and hub genes with R WGCNA.

TianGzlab/OmicsClaw

Constraint-based (COBRA) analysis of genome-scale metabolic models: FBA, FVA, knockouts, flux sampling, production envelopes, gapfilling, media optimization.

jaechang-hits/SciAgent-Skills

Build or update Grain's interactive component genome. An agent skill from ObneyAI/grain.

ObneyAI/grain

Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome.

BioTender-max/awesome-bio-agent-skills

Fetch a regional slice of plasma pQTL summary statistics from the UK Biobank Pharma Proteomics Project (UKB-PPP; Sun 2023 Nature) for a specific (protein, ancestry) measurement.

ClawBio/ClawBio

Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms.

google-deepmind/science-skills

ASURAT is a software for single-cell data analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb.

bioMate-AI/biomate-bioconductor-kb

Use local ancestry reference-panel tools for 1000 Genomes GRCh37/GRCh38 PCA projection, marker overlap QC, and qualitative reference-neighbor context.

exon-research/genomi

Sort alignment files by coordinate or read name using samtools and pysam.

GPTomics/bioSkills

Meta-agent that routes bioinformatics requests to specialised sub-skills.

ClawBio/ClawBio

Stage 3 of the spatial transcriptomics workflow — identify spatial domains and detect spatially variable genes.

QING1105/ezST

Load when comparing gene expression between two conditions in bulk RNA-seq count data.

TianGzlab/OmicsClaw

BioMaster conversational bioinformatics assistant; starts workflows only after execution intent or empty activation.

ai4nucleome/BioMaster

We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples.

bioMate-AI/biomate-bioconductor-kb

Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC…

K-Dense-AI/scientific-agent-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

Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression.

K-Dense-AI/scientific-agent-skills

Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis.

K-Dense-AI/scientific-agent-skills

Builds, registers, debugs, and operates bioinformatics workflows on Latch using the Python SDK, CLI, Latch Data and Registry, Nextflow, Snakemake, programmatic execution, and Latch MCP.

K-Dense-AI/scientific-agent-skills

Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces gene hit rankings with effect…

K-Dense-AI/scientific-agent-skills

Processes, cleans, compares, and searches tandem mass spectra with matchms.

K-Dense-AI/scientific-agent-skills

Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs.

K-Dense-AI/scientific-agent-skills

Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies.

K-Dense-AI/scientific-agent-skills

Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results.

K-Dense-AI/scientific-agent-skills

Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR correction, coefficient-matched LFC shrinkage…

K-Dense-AI/scientific-agent-skills

Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts.

K-Dense-AI/scientific-agent-skills

Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.

GPTomics/bioSkills

Ancestry decomposition PCA against the Simons Genome Diversity Project

ClawBio/ClawBio

Stage 4 of the spatial transcriptomics workflow — deconvolve Visium spots into cell-type proportions.

QING1105/ezST

Register, parse, and digitize private genome source files into a local Active Genome Index and supporting evidence stores.

exon-research/genomi

Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.

TianGzlab/OmicsClaw

Queries the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants.

K-Dense-AI/scientific-agent-skills

Applies the computational biology and AI-driven reasoning of Aviv Regev (computational biologist, Genentech, single-cell genomics).

K-Dense-AI/mimeographs

Performs Scanpy single-cell RNA-seq QC, normalization, HVG selection, PCA/UMAP/t-SNE, clustering, exploratory marker ranking, pseudobulk preparation, visualization, and Seurat or…

K-Dense-AI/scientific-agent-skills

Constructs deep-links and URLs for the AlphaGenome Atlas website.

google-deepmind/science-skills