Skill Claude CodeCodex
Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation. Skip single-batch inputs; use sc-batch-integration for single-cell data or spatial-integrate for spatial slices.
Skill Claude CodeCodex
Load when discovering bulk gene co-expression modules and hub genes with R WGCNA. Skip direct expression contrasts (use bulkrna-de), existing-gene-list PPI lookup (use bulkrna-ppi-network), or single-cell networks (use sc-grn).
Skill Claude CodeCodex
Load when comparing gene expression between two conditions in bulk RNA-seq count data. Skip when the data is single-cell (use sc-de); spatial (use spatial-de); you need exon-level alternative splicing (use bulkrna-splicing).
Skill Claude CodeCodex
Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference. Skip when the data is already single-cell (no deconvolution needed); spatial deconvolution (use spatial-deconv).
Skill Claude CodeCodex
Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list. Skip when the input is single-cell (use sc-enrichment); the input is spatial (use spatial-enrichment); metabolite pathways (use metabolomics-pathway-enrichment).
Skill Claude CodeCodex
Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference. Skip when IDs already match downstream needs; use fetchmapping explicitly for MyGene lookup.
Skill Claude CodeCodex
Load when querying STRING for the protein-protein interaction neighborhood of a bulk RNA-seq DEG list and finding hub genes. Skip when pathway enrichment of the same list (use bulkrna-enrichment); de novo co-expression network discovery (use bulkrna-coexpression).
Skill Claude CodeCodex
Load when checking a bulk RNA-seq count matrix for library-size outliers, gene detection rates, and sample-sample correlation before DE. Skip when data is raw FASTQ (use bulkrna-read-qc); aligner logs (use bulkrna-read-alignment); single-cell counts (use sc-qc).
Skill Claude CodeCodex
Load when summarising STAR / HISAT2 / Salmon alignment-rate logs in bulk RNA-seq. Skip when data is raw FASTQ (use bulkrna-read-qc); already counted (use bulkrna-qc); genome-DNA alignment (use genomics-alignment).
Skill Claude CodeCodex
Load when checking raw FASTQ quality (Phred / GC / adapter / Q20-Q30) before alignment in bulk RNA-seq. Skip when reads are already aligned (use bulkrna-read-alignment); counted (use bulkrna-qc); single-cell FASTQ (use sc-fastq-qc).
Skill Claude CodeCodex
Load when summarising rMATS / SUPPA2 alternative-splicing output and identifying significant differential splicing events. Skip when you only have count-level DE (use bulkrna-de); splicing in single-cell; spatial data (currently unsupported).
Skill Claude CodeCodex
Load when comparing bulk expression strata against clinical time-to-event data with Kaplan-Meier and log-rank tests. R survival also fits Cox HR; Python reports a descriptive events/person-time ratio. Skip missing clinical outcomes.
Skill Claude CodeCodex
Load when placing bulk RNA-seq samples on a single-cell reference's pseudotime axis (NNLS deconvolution + nearest-neighbour mapping). Skip when plain cell-type proportions (use bulkrna-deconvolution); native single-cell trajectory inference (use sc-pseudotime).
Skill Claude CodeCodex
Load when computing alignment QC metrics (mapping rate, MAPQ distribution, insert size, duplicate rate, proper-pair rate) from a text SAM file produced by any short-/long-read aligner (BWA / Bowtie2 / Minimap2); convert a BAM with samtools view -h first. Skip when running the alignment step itself; only FASTQ-level QC…
Skill Claude CodeCodex
Load when computing genome-assembly QC metrics — N50/N90, L50/L90, total length, contig count, GC content, longest-contig — from a FASTA produced by any assembler (SPAdes / Megahit / Flye / Canu). Skip when running the assembly itself; assessing alignment quality (use genomics-alignment).
Skill Claude CodeCodex
Load when calling CNV segments via CBS-style segmentation on a bin-level log2-ratio CSV from exome / WGS coverage — emits per-segment 5-class CN state (amplification / gain / neutral / loss / deepdeletion), per-chromosome summary, genome-fraction-altered. Skip when working with single-cell / spatial CNV (use…
Skill Claude CodeCodex
Load when summarising a peak file (BED / narrowPeak) from ATAC-seq / ChIP-seq / CUT&Tag — peak count, width distribution, per-chromosome counts, score statistics. Skip when calling peaks from BAM (run MACS / Genrich externally first); working with single-cell ATAC (use scatac-preprocessing).
Skill Claude CodeCodex
Load when summarising a phased VCF (output of WhatsHap / SHAPEIT5 / Eagle2) — phased fraction of het variants, phase-block N50, PS-field parsing, pipe-delimited genotype detection. Skip when the input is unphased (run a phaser first); calling small variants (use genomics-variant-calling).
Skill Claude CodeCodex
Load when running pre-alignment FASTQ quality control — Phred quality scores, Q20/Q30 rates, GC / N content, read-length distribution, adapter-contamination detection. Skip when working with already-aligned BAMs (use genomics-alignment); peak / variant files are the input (use the relevant downstream skill).
Skill Claude CodeCodex
Load when summarising structural variants from an SV VCF (DEL / DUP / INV / TRA) — INFO/SVTYPE-based classification, size classification, per-type counts. Skip when working with small SNVs / indels (use genomics-variant-calling); calling SVs from BAM (run Manta / Delly / Sniffles first).
Skill Claude CodeCodex
Load when summarising functional impact of an annotated variant CSV — per-IMPACT counts (HIGH / MODERATE / LOW / MODIFIER), top consequences, gene-affected count. Skip when input is a raw VCF (convert with bcftools +split-vep first); calling raw variants (use genomics-variant-calling); filtering VCFs (use…
Skill Claude CodeCodex
Load when summarising small variants (SNVs / indels) from a VCF or computing demo-pattern variant statistics (Ti/Tv ratio, per-chromosome distribution, SNP / indel split). Skip when filtering / merging VCFs (use genomics-vcf-operations); calling structural variants (use genomics-sv-detection); adding functional…
Skill Claude CodeCodex
Load when summarising / filtering a VCF — variant classification (SNP / MNP / INS / DEL / COMPLEX), Ti/Tv ratio, QUAL / DP threshold filtering, INFO-field parsing. Skip when calling variants from BAM (run an external caller first); adding functional annotations (use genomics-variant-annotation).
Skill Claude CodeCodex
Load when extracting GEO accessions, dataset metadata, and downloadable references from a scientific paper (PDF / URL / DOI / PubMed ID / raw text) for downstream omics analysis. Skip when the dataset is already in hand; the paper names no dataset to fetch.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: