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    32 repositories

    • CSI-Microbes-identification

      Public
      Code for the identification step for CSI-Microbes
      Python
      •
      Other
      •7•27•0•0•Updated Nov 25, 2024Nov 25, 2024

    • ProcessTrialtrove

      Public
      Software for analyzing the data in the trialtrove database
      Python
      •1•0•0•0•Updated Nov 23, 2024Nov 23, 2024

    • 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 2020), including equivalent models using TCGA RNA-seq gene expression and combined microbial abundance and gene expression for comparison.
      cancergene-expressioncancer-genomicsmicrobiometumor-microenvironmenttumor-biomarkerstumor-microbiome
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •9•14•0•0•Updated Nov 13, 2024Nov 13, 2024

    • tcga-wgs-kraken-microbial-quant

      Public
      Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data
      metagenomicsbioinformatics-pipelinesnakemake-workflowmetagenomic-pipelinesnakemake-pipelinebioinformatics-workflowmetagenomics-taxon-profiling
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 3, 2024Nov 3, 2024

    • MORSE

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • DECODEM

      Public
      Investigate the predictive power of the TME for patient response in a cell-type-specific manner
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 22, 2024Jun 22, 2024

    • CSI-Microbes-analysis

      Public
      The code for running the analysis component of CSI-Microbe
      Python
      •3•12•0•0•Updated Jan 3, 2024Jan 3, 2024

    • SAHMI

      Public
      SAHMI fork for CSI-Microbes comparison
      R
      •
      Other
      •13•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • RNA-snakemake-rules

      Public
      Snakemake rules written for RNA-seq
      Python
      •1•0•0•0•Updated Nov 27, 2023Nov 27, 2023

    • PERCEPTION

      Public
      Utilizing single-cell omics from patients tumor to predict response and resistance.
      14•62•4•1•Updated Apr 25, 2023Apr 25, 2023

    • drug.OnTarget

      Public
      Identifying drug targets by integrating large-scale drug and genetic screens.
      HTML
      •2•0•1•0•Updated Mar 3, 2023Mar 3, 2023

    • Tcell_Ucp2

      Public
      R
      •0•0•0•0•Updated Feb 11, 2023Feb 11, 2023

    • madhitter

      Public
      Python
      •
      GNU General Public License v3.0
      •0•9•0•0•Updated Jan 9, 2023Jan 9, 2023

    • car22-hlh

      Public
      Code to reproduce analysis for 'Biomarkers Associated with Hemophagocytic Lymphohistiocytosis-Like Toxicities Provide Novel Insights into CD22 CAR T-Cell Inflammatory Responses'. Lichtenstein et al., 2020
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 8, 2022Mar 8, 2022

    • gembox

      Public
      In-house toolbox for genome-scale metabolic modeling (GEM) for the Ruppin lab
      R
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Mar 2, 2022Mar 2, 2022

    • 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
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 21, 2022Feb 21, 2022

    • sksurv-bio-workflows

      Public
      Framework to build, evaluate, select, and compare ML survival analysis models using high-dimensional biological data and other covariates
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Feb 21, 2022Feb 21, 2022

    • sklearn-extensions

      Public
      scikit-learn extensions
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 21, 2022Feb 21, 2022

    • covid_metabolism

      Public
      Metabolic modeling of SARS-CoV-2 infection and antiviral target prediction
      R
      •2•2•0•0•Updated Dec 21, 2021Dec 21, 2021

    • sksurv-extensions

      Public
      scikit-survival extensions
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Dec 16, 2021Dec 16, 2021

    • Immune_determinant_for_power_of_TMB

      Public
      HTML
      •1•3•0•0•Updated Dec 15, 2021Dec 15, 2021

    • Rcplex2

      Public
      Adding minor functions to the CRAN Rcplex package
      Shell
      •7•1•0•0•Updated Nov 22, 2021Nov 22, 2021

    • aml-2019

      Public
      Reproducible analysis in collaboration with Ani Deshpande Lab
      0•0•0•0•Updated Nov 15, 2021Nov 15, 2021

    • crispr_risk

      Public
      Our study systematically charts and points to the potential selection of specific cancer drivers mutation during CRISPR-Cas9 gene editing.
      HTML
      •0•1•0•0•Updated Sep 6, 2021Sep 6, 2021

    • apa_lung

      Public
      HTML
      •0•0•0•0•Updated Jun 22, 2021Jun 22, 2021

    • pathogen-discovery-rules

      Public
      Python
      •1•2•1•0•Updated May 10, 2021May 10, 2021

    • scSigR-1

      Public
      Generate signature matrix from single cell data.
      R
      •
      MIT License
      •7•0•0•0•Updated Apr 13, 2021Apr 13, 2021

    • scSigR

      Public
      Generate signature matrix from single cell data.
      R
      •
      MIT License
      •7•8•2•0•Updated Apr 13, 2021Apr 13, 2021

    • ACE2_modulating_drugs

      Public
      Identification of ACE2 expression-modulating drugs
      R
      •2•1•0•0•Updated Jun 15, 2020Jun 15, 2020

    • EGFR_NSCLC_ICB_analysis

      Public
      R markdown scripts containing analyses aimed at identifying the relative contribution of EGFR mutant status and TMB to immunotherapy response
      0•2•0•0•Updated Jun 14, 2020Jun 14, 2020