Pinned Repositories
ACE2_modulating_drugs
Identification of ACE2 expression-modulating drugs
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
BDK-iRWR
An improved random walk -based method on prioritizing cancer genes based on cancer-specific network
BioinfoHub
Blasso
Integrating LASSO and bootstrapping algorithm to find best prognostic or predictive biomarkers
BLUPHAT
CAIT
Code for Covariate Adjusted Interaction Trees
CAncer-bioMarker-Prediction-Pipeline-CAMPP
The Cancer bioMarker Prediction Pipeline (CAMPP)
cancer_drug_response
TDA-cancerSubtypes
Topological Approach for Cancer Subtyping from Gene Expression Data
Xudeh's Repositories
Xudeh/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Xudeh/Blasso
Integrating LASSO and bootstrapping algorithm to find best prognostic or predictive biomarkers
Xudeh/CancerSubtypesPrognosis
Cancer subtypes and prognosis based on multiple transcriptomic data sets
Xudeh/cmapR
Tools for manipulating annotated data matrices
Xudeh/coloc
Repo for the R package coloc
Xudeh/DeathsOfDespair
Analysis of deaths from alcohol-specific causes, drugs and suicide
Xudeh/easyConvert
Easily convert Gene ID
Xudeh/gdscIC50
An R package to fit dose response curves for data from the Genomics of Drug Sensitivity of Cancer (GDSC) project.
Xudeh/GMM
Gaussian Mixture Model clustering (Rasmussen, 1999)
Xudeh/GOSemSim
:golf: GO-terms Semantic Similarity Measures
Xudeh/graphlayouts
new layout algorithms for network visualizations in R
Xudeh/HMM
Hidden Markov Model clustering (Lin and Li, 2017)
Xudeh/IOBR
IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.
Xudeh/MOVICS
Multi-Omics integration and VIsualization in Cancer Subtyping
Xudeh/netrankr
An R package for network centrality
Xudeh/oncoPredict
Xudeh/PCaDB
PCaDB - a comprehensive and interactive database for transcriptomes from prostate cancer population cohorts
Xudeh/PCaSignatures
Comprehensive evaluation of machine learning models and gene expression signatures for prostate cancer prognosis
Xudeh/PLSDA
PluMA plugin that runs Partial Least Squares Discriminant Analysis (PLS-DA, Stahle and Wold 1987)
Xudeh/PluMA
A lightweight and flexible analysis pipeline
Xudeh/pvalueTex
Supplementary Material of manuscript, and Cutoff Finding R script
Xudeh/R-graph-gallery
A website that displays hundreds of R charts with their code
Xudeh/Rcpi
Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
Xudeh/roughnet
R package to draw sketchy, hand-drawn-like networks with roughjs
Xudeh/SPLSDA
Sparse Partial Least Squares Differential Analysis (SPLSDA) (LeCao et al, 2011)
Xudeh/Stacked_SGL
Xudeh/tcga-microbiome-prediction
Predictive models of cancer prognosis and drug response using tumor microbial abundances derived from WGS and RNA-seq sequencing data for 32 TCGA cancers (Poore et al. Nature 2020), including equivalent models using RNA-seq gene expression data as well as models combining both tumor microbial abundances and gene expression for comparison.
Xudeh/UCSCXenaTools
:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
Xudeh/UpSetR
An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
Xudeh/XGBLC