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Selects biomarker features from high-dimensional omics data using Boruta all-relevant selection, mRMR, LASSO/elastic-net, and stability selection, while controlling the leakage, irreproducibility, and correlated-feature traps that make most published signatures fail to replicate. Use when identif...
Infers dynamic gene regulatory networks from bulk time-series expression data using Granger causality (statsmodels), dynGENIE3 (Extra-Trees on ODE-derived expression derivatives), and dynamic Bayesian networks (bnlearn). Identifies time-delayed regulatory relationships and tracks network rewiring...
Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for...
Estimate SNP heritability and partition it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability...
Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outco...
Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, con...
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 and 2.0. Use when working with PLINK format files or running QC.
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with limma (default) or MSstats for complex feature-level designs. Use when processing mass spectrometry proteomics.
Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (s...
Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution instruments) to report absolute concentrations. Covers the internal-standard strategy (external cal -> global IS -> standard addition -> stable-isotope-labeled IS), weighted calib...
Models continuous temporal trajectories from bulk or time-resolved omics data using generalized additive models (mgcv), spline regression, and changepoint detection (segmented, ruptures). Fits smooth gene expression curves and tests trajectory differences between conditions. Use when fitting non-...
End-to-end time-course analysis from expression matrix to temporal patterns and enrichment. Covers temporal DE, Mfuzz soft clustering, optional rhythm detection, GAM trajectory fitting, and per-cluster pathway enrichment. Use when analyzing bulk time-series expression experiments from any omics p...
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