gosianow

CMSclassifier

crcsc

CRC Subtyping Consortium

SigProfilerAssignmentR

R wrapper for utilizing the SigProfilerAssignment framework

SigProfilerAssignment

Assignment of known mutational signatures to individual samples and individual somatic mutations

alphafold

Open source code for AlphaFold.

chrysalis

Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.

Qin-CardosoRodriguez-et-al

Scripts and notebooks for Qin & Cardoso Rodriguez et al

xCell

Cell types enrichment analysis

Kassandra

Bostongene cell deconvolution algorithm from RNAseq

CMScaller

CountClust

A R package for Grade of Membership model and Visualization of counts data:

ACTIONet

ACTIONet single-cell analysis framework

stardist

StarDist - Object Detection with Star-convex Shapes

emp_programs

Code used in the manuscript "Transcriptional census of epithelial-mesenchymal plasticity in cancer"

crc-immune-hubs

Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organized multicellular immune hubs in human colorectal cancer"

cNMF

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

celda

Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data

SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

liger

R package for integrating and analyzing multiple single-cell datasets

pnet_prostate_paper

P-NET, Biologically informed deep neural network for prostate cancer classification and discovery

sfaira

data and model repository for single-cell data

scell_lung_adenocarcinoma

This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset

UCell

Gene set scoring for single-cell data

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

lollipops

This is the development fork - Stable code has been moved to ==>

cutpointr

Optimal cutpoints in R: determining and validating optimal cutpoints in binary classification

project-directory

Setting up a new project directory in the terminal or R

knitr

A general-purpose tool for dynamic report generation in R

seqtk

Toolkit for processing sequences in FASTA/Q formats

docopt.R

Command-line interface description language for R (http://docopt.org)