Best bioinformatics skills, page 22

Automate gene expression analysis with the GenoMAS multi-agent system

wentorai/research-plugins

Workflows for RNA-seq, GWAS, and variant calling in genomic research

wentorai/research-plugins

Benchmark for LLM agents on gene expression data analysis. An agent skill from wentorai/research-plugins.

wentorai/research-plugins

AI research assistant for biomedicine, RNA-seq, and drug discovery

wentorai/research-plugins

Access genomes, genes, and taxonomy data via NCBI Datasets v2 API

wentorai/research-plugins

Decision framework for manual marker-based, automated (CellTypist), and reference-based (popV) cell type annotation in scRNA-seq.

BioTender-max/awesome-bio-agent-skills

Local Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and optional two-group differential expression from raw-count .h5ad.

FreedomIntelligence/OpenClaw-Medical-Skills

Retrieve genomic sequences from Ensembl database using transcript or gene IDs to obtain nucleotide and protein sequences.

InternScience/scp

Retrieve gene information from NCBI Gene database by gene IDs to obtain genomic details, function, and expression data.

InternScience/scp

Search for similar protein sequences in UniProt Swiss-Prot database using BLAST to identify homologous proteins and functional relationships.

InternScience/scp

Query IGVF Catalog for regulatory element–gene associations within a genomic region, including association scores, element types, and biosample context.

InternScience/scp

Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns.

InternScience/scp

Retrieve protein sequences and functional information from UniProt database by protein name, enabling protein analysis and bioinformatics workflows.

InternScience/scp

Query dbSNP + NCBI Gene to get variant genomic position (chromosome, coordinates, ref/alt alleles, mutation type) and associated gene coordinates.

InternScience/scp

Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples.

jaechang-hits/SciAgent-Skills

Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline.

jaechang-hits/SciAgent-Skills

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug…

jaechang-hits/SciAgent-Skills

Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x).

jaechang-hits/SciAgent-Skills

Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API.

jaechang-hits/SciAgent-Skills

Bulk RNA-seq DE with R/Bioconductor DESeq2. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

ENA REST API for sequences, reads, assemblies, and annotations.

jaechang-hits/SciAgent-Skills

gnomAD v4 population variant frequencies via GraphQL API. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping.

jaechang-hits/SciAgent-Skills

De novo and known TF motif enrichment in ChIP-seq/ATAC-seq peaks via HOMER.

jaechang-hits/SciAgent-Skills

Query InterPro REST API for protein domain architecture, family classification, and member-DB integration.

jaechang-hits/SciAgent-Skills

MaxQuant + Perseus proteomics pipeline: run MaxQuant for LFQ and SILAC; parse proteinGroups.txt in Python; filter contaminants/decoys; log2 + median-normalize; impute MNAR; t-test with FDR; volcano…

jaechang-hits/SciAgent-Skills

Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations.

jaechang-hits/SciAgent-Skills

Three-tiered approach to omics data analysis (transcriptomics, proteomics) covering validated pipelines, standard workflows, and custom methods

jaechang-hits/SciAgent-Skills

Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline.

jaechang-hits/SciAgent-Skills

Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline.

jaechang-hits/SciAgent-Skills

Three-tiered sgRNA design guide using validated Addgene sequences, CRISPick pre-computed datasets, or de novo design rules for CRISPR experiments

jaechang-hits/SciAgent-Skills

Annotate and filter VCF variants with SnpEff and SnpSift. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download…

jaechang-hits/SciAgent-Skills

Create or maintain a portable learning vault for any certification, course, or study goal.

glebis/claude-skills

A skill your agent uses for OmicVerse bulk RNA-seq, enrichment/signature scoring, metabolomics, proteomics, microbiome, and statistical table workflows.

VectorSpaceLab/AREX-Skill

A skill your agent uses for OmicVerse spatial transcriptomics, histology-to-spatial prediction, deconvolution, cell mapping, tissue zones, spatial IO, and spatial-adjacent multimodal integration.

VectorSpaceLab/AREX-Skill

Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.

BioTender-max/awesome-bio-agent-skills

Rust-backed Python library for fast genomic token arithmetic and BED processing.

jaechang-hits/SciAgent-Skills

Python library for genomic interval ML. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Selects, investigates, and compares AWS object, file, and block storage services, and answers cost, performance, configuration, security, and troubleshooting questions about storage services.

aws/agent-toolkit-for-aws

24 biomedical research skills. An agent skill from wentorai/research-plugins.

wentorai/research-plugins

Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities.

bioMate-AI/biomate-bioconductor-kb

This package provides the visualization of bayesian network inferred from gene expression data.

bioMate-AI/biomate-bioconductor-kb

The package CellBarcode performs Cellular DNA Barcode analysis.

bioMate-AI/biomate-bioconductor-kb

The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries.

bioMate-AI/biomate-bioconductor-kb

ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis.

bioMate-AI/biomate-bioconductor-kb

cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set.

bioMate-AI/biomate-bioconductor-kb