Ruppin Lab

PERCEPTION

Utilizing single-cell omics from patients tumor to predict response and resistance.

CSI-Microbes-identification

Code for the identification step for CSI-Microbes

tcga-microbiome-prediction

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.

madhitter

scSigR

Generate signature matrix from single cell data.

CSI-Microbes-analysis

The code for running the analysis component of CSI-Microbe

Immune_determinant_for_power_of_TMB

covid_metabolism

Metabolic modeling of SARS-CoV-2 infection and antiviral target prediction

EGFR_NSCLC_ICB_analysis

R markdown scripts containing analyses aimed at identifying the relative contribution of EGFR mutant status and TMB to immunotherapy response

pathogen-discovery-rules

SingleCellSimulate

The following repository contains the R code to simulate 4 single cell RNASeq datasets that were used to test the performance of deconvolution

ACE2_modulating_drugs

Identification of ACE2 expression-modulating drugs

crispr_risk

Our study systematically charts and points to the potential selection of specific cancer drivers mutation during CRISPR-Cas9 gene editing.

Rcplex2

Adding minor functions to the CRAN Rcplex package

sksurv-bio-workflows

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

car22-hlh

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

drug.OnTarget

Identifying drug targets by integrating large-scale drug and genetic screens.

gembox

In-house toolbox for genome-scale metabolic modeling (GEM) for the Ruppin lab

Tcell_Ucp2

aml-2019

Reproducible analysis in collaboration with Ani Deshpande Lab

apa_lung

DECODEM

Investigate the predictive power of the TME for patient response in a cell-type-specific manner

MORSE

ProcessTrialtrove

Software for analyzing the data in the trialtrove database

RNA-snakemake-rules

Snakemake rules written for RNA-seq

SAHMI

SAHMI fork for CSI-Microbes comparison

scSigR-1

Generate signature matrix from single cell data.

sklearn-bio-workflows

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

sklearn-extensions

scikit-learn extensions

sksurv-extensions

scikit-survival extensions