GitHub
bio-variant-annotation
Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance.
☆ 299View skill
tools bioinformatics AI Skills
Discover tools bioinformatics skills, compare source repositories and read the instructions for each workflow.
Categories: tools bioinformatics
tools bioinformatics Clear filters
Browse skills
GitHub
bio-genome-assembly-hifi-assembly
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully reso...
☆ 299View skill
GitHub
bio-workflows-expression-to-pathways
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
☆ 299View skill
GitHub
bio-database-access-uniprot-access
Access UniProt protein database for sequences, annotations, and functional information. Use when you need protein data, GO terms, domain annotations, or protein-protein interactions.
☆ 299View skill
GitHub
bio-copy-number-cnv-annotation
Annotate CNVs with genes, pathways, and clinical significance. Use to interpret CNV calls and identify affected genes.
☆ 299View skill
GitHub
bio-proteomics-spectral-libraries
Build, manage, and search spectral libraries for proteomics. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.
☆ 299View skill
GitHub
bio-restriction-fragment-analysis
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests.
☆ 299View skill
GitHub
bio-metagenomics-strain-tracking
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, tra...
☆ 299View skill
GitHub
bio-chipseq-differential-binding
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values.
☆ 299View skill
GitHub
bio-workflows-proteomics-pipeline
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma.
☆ 299View skill
GitHub
bio-pdb-structure-navigation
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use for accessing models, chains, residues, and atoms, iterating over structure levels, extracting sequences, identifying residue types,...
☆ 299View skill
GitHub
bio-data-visualization-genome-tracks
Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV. Use when visualizing genomic data at specific loci with multiple aligned tra...
☆ 299View skill
GitHub
bio-chipseq-visualization
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions.
☆ 299View skill
GitHub
bio-read-alignment-star-alignment
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Use for RNA-seq data requiring splice-aware alignment. Supports two-pass mode for novel splice junction discovery.
☆ 299View skill
GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
☆ 283View skill
GitHub
nextflow-development
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core,...
☆ 210View skill
GitHub
single-cell-rna-qc
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering lo...
☆ 210View skill
GitHub
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS sys...
☆ 210View skill
GitHub
scvi-tools
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq mul...
☆ 210View skill
GitHub
claude-scientific-skills
Comprehensive collection of 128+ ready-to-use scientific skills for Claude enabling research across biology, chemistry, medicine, genomics, and advanced analysis domains.
☆ 129View skill
GitHub
fiftyone-embeddings-visualization
Visualize datasets in 2D using embeddings with UMAP or t-SNE dimensionality reduction. Use when users want to explore dataset structure, find clusters in images, identify outliers, color samples by class or met...
☆ 124View skill
GitHub
fiftyone-find-duplicates
Find duplicate or near-duplicate images in FiftyOne datasets using brain similarity computation. Use when users want to deduplicate datasets, find similar images, cluster visually similar content, or remove red...
☆ 124View skill
GitHub
project-research
Research workflow patterns specific to {project}. Covers research agent coordination, source management, and synthesis strategies.
☆ 122View skill
GitHub
lifecycle
Guidance for managing R package lifecycle according to tidyverse principles using the lifecycle package. Use when: (1) Setting up lifecycle infrastructure in a package, (2) Deprecating functions or arguments, (...
☆ 94View skill
The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.