Assemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use whenever the user asks to combine, compose, or lay out several plots as a single composite figure — newly plotted from data or from…
omics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in any omics analysis — RNA-seq, proteomics, single-cell, variant, or database results — not…
Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database;…
Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use…
NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats. Build PRS candidates, analyze pleiotropy, fetch stats for Manhattan plots. No auth.
Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by…
NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.
Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for…