Best bioinformatics skills, page 18

Machine learning toolkit for genomic interval (BED) data; use it when you need to tokenize BED collections and train embeddings for regions/cells/labels, build consensus peak universes, or run…

aipoch/medical-research-skills

A high-performance Rust toolkit (with Python bindings and a CLI) for genomic interval analysis; use it when you need fast overlap queries, coverage track generation, genomic tokenization for ML…

aipoch/medical-research-skills

Professional beautification tool for gene expression heatmaps, automatically adds clustering trees, color annotation tracks, and intelligently optimizes label layout.

aipoch/medical-research-skills

Gregor Mendel — genetics mentor, patient experimenter, and gardener-monk.

aipoch/medical-research-skills

Analyze data with metagenomic-krona-chart using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

aipoch/medical-research-skills

Designs complete research plans that integrate clinical variables with multi-omics data from a user-provided biomedical direction.

aipoch/medical-research-skills

Check if referenced bioinformatics software/code licenses allow commercial use (GPL vs MIT, etc.).

aipoch/medical-research-skills

Analyze data with phylogenetic-tree-styler using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

aipoch/medical-research-skills

Analyze data with pseudotime-trajectory-viz using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

aipoch/medical-research-skills

A Python bioinformatics toolkit for sequence, phylogeny, and microbiome/community-ecology analysis; use it when you need to compute diversity/ordination/statistics from biological data and standard…

aipoch/medical-research-skills

Designs complete single-cell research plans from a user-provided biomedical direction.

aipoch/medical-research-skills

Programmatically query public single-cell study metadata from the Broad Institute Single Cell Portal REST API when you need to search and filter datasets by organism, tissue, disease, or cell type…

aipoch/medical-research-skills

A medical-research-native literature reading skill for users with clinical, bioinformatics, translational, and basic experimental backgrounds.

aipoch/medical-research-skills

Estimates haplotype phase from population linkage disequilibrium with SHAPEIT5, SHAPEIT4, Eagle2, or Beagle - turning unphased genotypes (0/1) into phased haplotypes (0|1) for imputation input…

GPTomics/bioSkills

Selects and prepares the reference panel that phasing/imputation copies haplotypes from (1000 Genomes, HRC, TOPMed, HGDP+1kGP/gnomAD, CAAPA), matching panel ancestry to the target, reconciling…

GPTomics/bioSkills

Анализирует генетические данные пользователя из VCF файла. An agent skill from artwist-polyakov/polyakov-claude-skills.

artwist-polyakov/polyakov-claude-skills

GRN inference from expression via GRNBoost2 (gradient boosting) or GENIE3 (Random Forest).

jaechang-hits/SciAgent-Skills

Infer and visualize intercellular communication from scRNA-seq with CellChat (R).

jaechang-hits/SciAgent-Skills

Harmony batch correction for scRNA-seq and other omics. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Multi-Omics Factor Analysis v2 (MOFA+) with mofapy2. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Multi-modal single-cell analysis with muon/MuData. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scANVI), CITE-seq RNA+protein (totalVI), transfer learning (scARCHES), and DE with…

jaechang-hits/SciAgent-Skills

Analyse personal DNA / genome files for pharmacogenomics, disease risk, carrier status, ancestry and traits.

sammcj/agentic-coding

Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters.

FreedomIntelligence/OpenClaw-Medical-Skills

Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity.

FreedomIntelligence/OpenClaw-Medical-Skills

Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis.

FreedomIntelligence/OpenClaw-Medical-Skills

Test whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc.

FreedomIntelligence/OpenClaw-Medical-Skills

Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search.

FreedomIntelligence/OpenClaw-Medical-Skills

Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR.

FreedomIntelligence/OpenClaw-Medical-Skills

ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate…

FreedomIntelligence/OpenClaw-Medical-Skills

Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools.

FreedomIntelligence/OpenClaw-Medical-Skills

Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker.

FreedomIntelligence/OpenClaw-Medical-Skills

Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases.

FreedomIntelligence/OpenClaw-Medical-Skills

Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications.

FreedomIntelligence/OpenClaw-Medical-Skills

Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics.

FreedomIntelligence/OpenClaw-Medical-Skills

Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes.

FreedomIntelligence/OpenClaw-Medical-Skills

Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis.

FreedomIntelligence/OpenClaw-Medical-Skills

Detect copy number variants from targeted/exome sequencing using CNVkit.

FreedomIntelligence/OpenClaw-Medical-Skills

Statistical methods for calling hits in CRISPR screens. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis.

FreedomIntelligence/OpenClaw-Medical-Skills

Quality control for pooled CRISPR screens. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

FreedomIntelligence/OpenClaw-Medical-Skills

Creates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot.

FreedomIntelligence/OpenClaw-Medical-Skills

Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection.

FreedomIntelligence/OpenClaw-Medical-Skills

Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC.

FreedomIntelligence/OpenClaw-Medical-Skills

Quantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from BAM files.

FreedomIntelligence/OpenClaw-Medical-Skills

Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY.

FreedomIntelligence/OpenClaw-Medical-Skills

Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2.

FreedomIntelligence/OpenClaw-Medical-Skills

Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS.

FreedomIntelligence/OpenClaw-Medical-Skills