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1. sklearn-bio-workflows sklearn-bio-workflows Public

   Framework to build, evaluate, select, and compare ML classification and regression models using high-dimensional biological data and other covariates

   Python 2 1

2. sksurv-bio-workflows sksurv-bio-workflows Public

   Framework to build, evaluate, select, and compare ML survival analysis models using high-dimensional biological data and other covariates

   Python 1

3. dragonfish dragonfish Public

   A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG

   Python

4. ruppinlab/tcga-microbiome-prediction ruppinlab/tcga-microbiome-prediction Public

   Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-seq sequencing data for 32 TCGA cancers (Poore et al. Nature 2…

   Python 14 9

5. tcga-wgs-kraken-microbial-quant tcga-wgs-kraken-microbial-quant Public

   Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data

   Python

6. rna-seq-star-gex rna-seq-star-gex Public

   STAR + edgeR/DESeq2/limma-voom + GSEA RNA-seq gene expression analysis workflow

   Python