Best bioinformatics skills, page 21

GSEA and over-representation analysis (ORA) for RNA-seq and proteomics.

jaechang-hits/SciAgent-Skills

NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS.

jaechang-hits/SciAgent-Skills

KEGG REST API (academic only). An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

MS spectral matching and metabolite ID with matchms. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Aggregates QC from 150+ bioinformatics tools into one interactive HTML report.

jaechang-hits/SciAgent-Skills

GWAS and population genetics tool. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

protocols.io REST API: search and fetch wet-lab, bioinformatics, and clinical protocols by keyword, DOI, or category, with steps, reagents, materials, equipment, timing.

jaechang-hits/SciAgent-Skills

MS data processing with PyOpenMS for LC-MS/MS proteomics and metabolomics — mzML/mzXML I/O, signal processing (smoothing, peak picking, centroiding), feature detection/linking, peptide/protein ID…

jaechang-hits/SciAgent-Skills

Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM).

jaechang-hits/SciAgent-Skills

CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments.

jaechang-hits/SciAgent-Skills

Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables.

jaechang-hits/SciAgent-Skills

Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations.

jaechang-hits/SciAgent-Skills

Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions).

jaechang-hits/SciAgent-Skills

A skill your agent uses whenever you are reasoning about large-scale scientific projects, genomics, bioethics, data infrastructure, or long-term medical translation.

K-Dense-AI/mimeographs

Applies the operational and scientific frameworks of Stacey Gabriel (genomicist and sequencing platform leader at the Broad Institute).

K-Dense-AI/mimeographs

Generate Circos configuration files for circular genomics data visualization.

aipoch/medical-research-skills

Detect copy number variations from whole genome sequencing data and generate publication-quality genome-wide CNV plots.

aipoch/medical-research-skills

Process CRISPR screening data to identify essential genes and hit candidates.

aipoch/medical-research-skills

Auto-annotate cell clusters from single-cell RNA data using marker genes.

aipoch/medical-research-skills

Map spatial transcriptomics data from 10x Genomics Visium/Xenium onto.

aipoch/medical-research-skills

Bioinformatics workflow guide for sequence analysis, QC, plotting, structure rendering, and literature search.

DrugClaw/DrugClaw

Workflow for paired or integrated single-cell RNA and ATAC analysis with multimodal latent spaces and regulatory interpretation.

BioTender-max/awesome-bio-agent-skills

Multi-step KEGG bioinformatics workflows — pathway enrichment from gene lists, drug-target investigation, cross-species metabolic comparison, and compound-reaction network exploration.

davepoon/buildwithclaude

A skill your agent uses when targeting Genome Biology or deciding whether a genomics or computational biology manuscript fits this venue.

franklee16/academic-research-skills

A skill your agent uses when targeting Molecular Biology and Evolution (MBE) or deciding whether a molecular evolution manuscript fits this venue.

franklee16/academic-research-skills

A skill your agent uses when targeting Nature Genetics or deciding whether a genetics/genomics manuscript fits this venue.

franklee16/academic-research-skills

A skill your agent uses when targeting Nature Methods or deciding whether a methods/tools manuscript fits this venue.

franklee16/academic-research-skills

Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R.

aiskillstore/marketplace

Generates complete bidirectional multi-phenotype Mendelian randomization research designs from a user-provided exposure family and outcome family.

aipoch/medical-research-skills

Identifies translationally meaningful paths for bioinformatics findings by mapping omics or computational discoveries to diagnosis, stratification, prognosis, treatment-response, monitoring, or…

aipoch/medical-research-skills

Use Bio.Entrez to access NCBI databases (e.g., PubMed/GenBank) for searching, fetching summaries, and downloading records when your workflow needs to call the NCBI E-utilities API over the network.

aipoch/medical-research-skills

Generates complete comorbidity-oriented shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction.

aipoch/medical-research-skills

Generates complete conventional non-oncology bioinformatics research designs from a user-provided disease context, process-related gene family or biological theme, and validation direction.

aipoch/medical-research-skills

Generates complete conventional oncology bulk-transcriptome biomarker and hub-gene research designs from a user-provided cancer type and study direction.

aipoch/medical-research-skills

Generates complete cross-disease shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction.

aipoch/medical-research-skills

DNAnexus cloud genomics platform. An agent skill from aipoch/medical-research-skills.

aipoch/medical-research-skills

Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need…

aipoch/medical-research-skills

Generates complete phenotype-scoring bioinformatics research designs for any disease context and any user-defined phenotype, pathway, process, signature, or molecular program.

aipoch/medical-research-skills

This skill is applicable when using LaminDB. An agent skill from aipoch/medical-research-skills.

aipoch/medical-research-skills

Generates complete Mendelian Randomization + single-cell transcriptomics (scRNA-seq) research designs from a user-provided direction.

aipoch/medical-research-skills

Generates complete programmed-cell-death (PCD) / regulated-cell-death (RCD) bulk-transcriptome oncology research designs from a user-provided disease and mechanism theme.

aipoch/medical-research-skills

Generates complete process-related diagnostic biomarker bioinformatics research designs from a user-provided disease context, gene-family or pathway theme, and validation direction.

aipoch/medical-research-skills

Genomic file toolkit. An agent skill from aipoch/medical-research-skills.

aipoch/medical-research-skills

Generates complete conventional single-gene oncology research designs from a user-provided cancer context, target gene, and validation direction.

aipoch/medical-research-skills

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

OpenClaw bioinformatics skill library for genomics pipelines

wentorai/research-plugins

Query gene, sequence, and variant data via the Ensembl REST API

wentorai/research-plugins