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Skill Claude CodeCodex
Complete workflow for single-cell RNA-seq analysis using Seurat v5. Process raw data through quality control, normalization, clustering, and cell type annotation with publication-ready visualizations.
Skill Claude CodeCodex
Not for: Single-molecule FISH (MERFISH/Xenium), Slide-seq, or single-cell RNA-seq without spatial coordinates. For scRNA-seq, use scrnaseq-scanpy-core-analysis.
Skill Claude CodeCodex
Kaplan-Meier survival estimation, Cox proportional hazards regression, and risk stratification for clinical and real-world evidence (RWE) datasets.
Skill Claude CodeCodex
Identify transcription factors (TFs) driving observed differential expression by integrating ChIP-Atlas TF binding data (epigenomics) with RNA-seq DE results (transcriptomics). Ranks TFs by a combined regulatory score incorporating binding enrichment, target-DE overlap (Fisher's exact test), and directional…
Skill Claude CodeCodex
Load when removing batch effects from a multi-cohort bulk RNA-seq dataset using ComBat (R or Python implementation). Skip when there is only one batch; single-cell batch integration (use sc-batch-integration); spatial multi-slice integration (use spatial-integrate).
Skill Claude CodeCodex
Load when discovering gene co-expression modules and hub genes in a bulk RNA-seq cohort via WGCNA-style soft-thresholded networks. Skip when direct DE comparison (use bulkrna-de); PPI lookup of an existing gene list (use bulkrna-ppi-network); single-cell co-expression (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 gene identifiers between Ensembl, Entrez, and HGNC symbol in a bulk RNA-seq count matrix. Skip when the input is already in the desired identifier system; organisms outside human/mouse; non-bulk-counts inputs.
Skill Claude CodeCodex
Load when querying STRING for the protein-protein interaction subgraph induced by 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 stratifying patients by gene expression and testing for survival differences (Kaplan-Meier + Cox) in bulk RNA-seq. Skip when no time-to-event clinical data exists; non-bulk cohorts (single-cell / spatial survival is not supported).
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 SAM or BAM file produced by any short-/long-read aligner (BWA / Bowtie2 / Minimap2). Skip when running the alignment step itself; only FASTQ-level QC is needed (use genomics-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) — BND-notation parsing, 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).
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: