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Data & Analytics · By GPTomics
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 49 | Builds diagnostic and prognostic classifiers on omics feature matrices with regularized logistic regression, random forest, and gradient-boosted trees, handling the pn regime, batch shortcut… | GPTomics/ | 1.2k | 1 repo | ~4.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 50 | Explains ML predictions on omics data with SHAP, LIME, and permutation importance, handling the correlated-feature trap, the conditional-vs-interventional Shapley choice, and the… | GPTomics/ | 1.2k | 1 repo | ~4.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 51 | Builds and validates predictive time-to-event models on clinical and omics data with penalized Cox, random survival forests, gradient-boosted and deep survival models, and prediction-grade… | GPTomics/ | 1.2k | 1 repo | ~4.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 52 | Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers, distinct from steady-state pool… | GPTomics/ | 1.2k | 1 repo | ~3.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 53 | Assigns honest lipid annotation levels, designs class-based internal-standard quantification, and runs lipid-aware differential and enrichment analysis with lipidr, guarding against… | GPTomics/ | 1.2k | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 54 | Turns untargeted LC-MS/MS features (m/z, RT, MS/MS) into confidence-stratified metabolite annotations using spectral-library matching (matchms), in-silico tools (SIRIUS/CSI:FingerID, MetFrag) and… | GPTomics/ | 1.2k | 1 repo | ~4.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 55 | Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing values for untargeted LC-MS/GC-MS metabolomics, framing each step as a measurement… | GPTomics/ | 1.2k | 1 repo | ~5k | Automated safety check: Pass | MIT | 1 mo ago |
| 56 | Maps metabolomics results to biological pathways via over-representation (ORA), metabolite-set enrichment (MSEA/QEA), mummichog/PSEA on raw m/z peaks, and network-diffusion enrichment (FELLA), with… | GPTomics/ | 1.2k | 1 repo | ~4.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 57 | Decision-grade statistical analysis for metabolomics intensity tables. | GPTomics/ | 1.2k | 1 repo | ~5k | Automated safety check: Pass | MIT | 1 mo ago |
| 58 | Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution instruments) to report absolute concentrations. | GPTomics/ | 1.2k | 1 repo | ~5.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 59 | Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time… | GPTomics/ | 1.2k | 1 repo | ~4.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 60 | Turns a shotgun profiler table (MetaPhlAn relative abundance, Bracken counts, HUMAnN function tables) into honest figures and defensible community statistics with phyloseq, vegan, microViz, and… | GPTomics/ | 1.2k | 1 repo | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 61 | Computes DNA methylation age (DNAm age) and pace of aging by applying frozen elastic-net epigenetic clocks to a clean beta matrix with methylclock, dnaMethyAge, or methylCIPHER. | GPTomics/ | 1.2k | 1 repo | ~4.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 62 | Builds supervised and unsupervised multivariate integration across bulk omics blocks with mixOmics - sPLS for sparse pairwise correlation, DIABLO (block.splsda) for a multi-block discriminant… | GPTomics/ | 1.2k | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 63 | Tests a ranked gene vector for coordinated expression shifts in GO, KEGG, Reactome, or MSigDB gene sets with clusterProfiler's gseGO, gseKEGG, gsePathway, and GSEA (fgseaMultilevel engine), and… | GPTomics/ | 1.2k | 1 repo | ~5k | Automated safety check: Pass | MIT | 1 mo ago |
| 64 | Draw and export phylogenetic trees with Bio.Phylo plus matplotlib, and route rich figures to ggtree, ETE4, or iTOL. | GPTomics/ | 1.2k | 1 repo | ~5.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 65 | Computes linkage disequilibrium (r2, D', composite Rogers-Huff r2), prunes correlated variants, clumps GWAS summary statistics to lead SNPs, and defines haplotype blocks with PLINK 1.9/2.0 and… | GPTomics/ | 1.2k | 1 repo | ~4.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 66 | In-memory Python population genetics with scikit-allel - GenotypeArray/HaplotypeArray/AlleleCountsArray, diversity (pi, theta, Tajima's D), SFS, FST (Weir-Cockerham, Hudson, Patterson), f3/D… | GPTomics/ | 1.2k | 1 repo | ~5k | Automated safety check: Pass | MIT | 1 mo ago |
| 67 | Builds and manages DIA spectral libraries as peptide query parameters (precursor m/z, a few fragment m/z plus relative intensities, normalized RT, optional CCS), covering experimental DDA… | GPTomics/ | 1.2k | 1 repo | ~4.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 68 | Exports publication-ready figures with the correct vector/raster split, embedded editable fonts, color-space-robust palettes, and journal-correct sizing and resolution in matplotlib and ggplot2. | GPTomics/ | 1.2k | 1 repo | ~3.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 69 | Runs parameterized Jupyter notebooks as reproducible batch report generators with papermill, renders them to HTML/PDF with nbconvert, aggregates results across samples, and makes notebook outputs… | GPTomics/ | 1.2k | 1 repo | ~2.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 70 | Builds reproducible Quarto reports, presentations, and websites across R, Python, and Julia, with correct engine selection, cache-vs-freeze semantics, native cross-references, parameters, and… | GPTomics/ | 1.2k | 1 repo | ~2.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 71 | Build restriction maps showing enzyme cut positions and inter-site distances along DNA using Biopython Bio.Restriction. | GPTomics/ | 1.2k | 1 repo | ~2.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 72 | Quality control and exploration of RNA-seq count matrices before differential expression. | GPTomics/ | 1.2k | 1 repo | ~2.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 73 | Tests whether a proposed or predicted RNA secondary structure is supported by evolutionary covariation using R-scape, which scores compensatory substitutions against a phylogeny-aware null and… | GPTomics/ | 1.2k | 1 repo | ~2.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 74 | Calculate assembly and sequence statistics (N50/L50, auN, NG50/NGA50, length distribution, GC content with ambiguity handling, summary reports) using Biopython. | GPTomics/ | 1.2k | 1 repo | ~3.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 75 | Build the spatial neighbor graph that every downstream spatial statistic (Moran's I, neighborhood enrichment, co-occurrence, spatial domains) inherits, using Squidpy. | GPTomics/ | 1.2k | 1 repo | ~4.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 76 | Detects spatially variable genes, spatial autocorrelation, and cell-type colocalization for spatial transcriptomics using Squidpy with PySAL/esda for local statistics. | GPTomics/ | 1.2k | 1 repo | ~4.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 77 | Draws TCR/BCR repertoire figures - V-J chord/circos, CDR3 spectratype, clonal-space stratification, clonal tracking across timepoints, rarefaction/extrapolation curves, overlap heatmaps, and… | GPTomics/ | 1.2k | 1 repo | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 78 | Infers directed, time-delayed gene regulatory edges from BULK time-series expression using Granger causality (statsmodels VAR F-test), dynGENIE3 (tree ensembles regressing ODE-derived derivatives… | GPTomics/ | 1.2k | 1 repo | ~5k | Automated safety check: Pass | MIT | 1 mo ago |
| 79 | Filters germline and somatic variant callsets at the site and genotype level with GATK VQSR (VQSLOD, truth-sensitivity tranches), VETS/ScoreVariantAnnotations, NVScoreVariants, hard filters with… | GPTomics/ | 1.2k | 1 repo | ~5.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 80 | Compute and interpret VCF quality-control metrics (Ti/Tv, het/hom, novel/known, missingness, HWE, contamination, relatedness) with bcftools stats, vcftools, plot-vcfstats, and identity tools… | GPTomics/ | 1.2k | 1 repo | ~4.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 81 | End-to-end biomarker discovery workflow from expression data to validated biomarker panels. | GPTomics/ | 1.2k | 1 repo | ~4.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 82 | End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expressed cell populations. | GPTomics/ | 1.2k | 1 repo | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 83 | Orchestrates imaging mass cytometry from raw MCD acquisitions to patient-level spatial analysis, chaining steinbock preprocessing, Mesmer/Cellpose segmentation, single-cell quantification… | GPTomics/ | 1.2k | 1 repo | ~4.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 84 | Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalization, confidence-stratified annotation, permutation-validated statistics… | GPTomics/ | 1.2k | 1 repo | ~4.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 85 | Orchestrates the end-to-end bisulfite/EM-seq methylation pipeline from FASTQ to differentially methylated regions, chaining Trim Galore/fastp QC, Bismark alignment + deduplication, methylation… | GPTomics/ | 1.2k | 1 repo | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 86 | Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arcasHLA + LOHHLA), VEP annotation (Wildtype+Frameshift plugins) +… | GPTomics/ | 1.2k | 1 repo | ~4.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 87 | Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4… | GPTomics/ | 1.2k | 1 repo | ~7k | Automated safety check: Pass | MIT | 1 mo ago |
| 88 | Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing… | GPTomics/ | 1.2k | 1 repo | ~5.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 89 | Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. | GPTomics/ | 1.2k | 1 repo | ~5.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 90 | Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools… | GPTomics/ | 1.2k | 1 repo | ~8.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 91 | Extracts per-cytosine methylation calls from aligned bisulfite/EM-seq reads with bismarkmethylationextractor (Bismark BAM) or the aligner-agnostic MethylDackel/BISCUIT (bwa-meth BAM), producing the… | GPTomics/ | 1.2k | 1 repo | ~5.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 92 | Operates the QIIME2 framework as the glue for an amplicon analysis - the .qza/.qzv artifact model, semantic types (FeatureTable[Frequency], SampleData[PairedEndSequencesWithQuality]… | GPTomics/ | 1.2k | 1 repo | ~5.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 93 | Assigns taxonomy to amplicon ASVs/OTUs (16S, ITS, 18S) with a classifier conditioned on a reference database and primer region - DADA2 assignTaxonomy + addSpecies (RDP naive Bayes), DECIPHER IDTAXA… | GPTomics/ | 1.2k | 1 repo | ~6.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 94 | Turns an enrichResult or gseaResult from clusterProfiler/enrichplot into a figure that collapses or shows gene-set redundancy, using dotplot, barplot, cnetplot, emapplot, treeplot, ridgeplot… | GPTomics/ | 1.2k | 1 repo | ~5.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 95 | Frames Bayesian phylogenetics as approximating a posterior distribution over trees conditioned on data AND priors via an MCMC that must be proven to have converged, using MrBayes, BEAST2, RevBayes… | GPTomics/ | 1.2k | 1 repo | ~6.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 96 | Infers and describes population structure with PCA (plink2 --pca, smartpca/EIGENSOFT, FlashPCA2), model-based clustering (ADMIXTURE, fastSTRUCTURE), FST estimators (Weir-Cockerham vs Hudson), and… | GPTomics/ | 1.2k | 1 repo | ~5.6k | Automated safety check: Pass | MIT | 1 mo ago |
