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3ca

Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".

5years

adobe_illustrator

basic-r

bio

bisque

An R toolkit for estimation of cell composition from bulk expression data

brca_cell_atlas

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

cafclassification

cancer_biology

ccle_heterogeneity

cellmarker

chromatinanthra

Source code from the manuscript "Chromatin Regulators Mediate Anthracycline Sensitivity in Breast Cancer"

clustergvis

One-step to Cluster and Visualize Gene Expression Matrix

crc_scrnaseq

csf_aging

Single cell transcriptomics reveals cerebrospinal fluid immune dysregulation during healthy brain aging and cognitive impairment

doubletfinder

R package for detecting doublets in single-cell RNA sequencing data

dplyr

ewingsinglecelldataanalysis

Code accompanying the manuscript "Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution"

garnett

geneticcorrelation

geo

ggplot

ggplot2

An implementation of the Grammar of Graphics in R

ggplot2cheatsheet

A reproduction of the Beautiful Plotting in R: A ggplot2 cheatsheet by Zev Ross

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

humanbreastcellatlas

Repository for codes for the HBCA paper

infercnv

irls

Machine learning-based integrative analysis develops an immune-derived lncRNA signature for improving clinical outcomes in colorectal cancer

learning-book

mendelian_randomization