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aneuploidy_score

R package to calculate the Aneuploidy Score from Chromosome Arm-level SCNAs/Aneuploidies (CAAs) as outlined and expanded by Shukla et al. (https://doi.org/10.1038/s41467-020-14286-0)

bam2bedpe

convert bam to bedpe format

bamgineer

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

bca_atacseq_project

This repository contains custom code used for analysis in El Ghamrasni et al.,

braf_rapid_autopsy

Computational analysis for BRAF-mutant melanoma rapid autopsy project

btsc-glutaminase-weiss

Code for scRNAseq analysis in Restall et al., Cancer Research, 2020

cancer-scrna-integration

A comparison of data integration methods for single-cell RNA sequencing of cancer samples

captcr-til-tracking

cbio-auto-import

scripts used for auto importing new datasets into the cBioPortal database; live

cbio_import_utils

cbioportal

cBioPortal for Cancer Genomics

cbioportal-deployment

Stuff to help deploy cBioPortal with ansible

cbioportal-docs

cbioportal-documentation

cbioportal-frontend

React Frontend of cBioPortal :tada:

cbioportal-importer

python package to load cancer genomics data sets into the cbioportal database; not live

cbioportal-octane-overlay

The OCTANE branding for cBioPortal, as a war overlay

cbioportal-oidc-overlay

cbpmanager

Generate, manage and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics.

cbporganizer

Tool to help cbioportal study owners to organize their studies for publishing to cbioportal

cfmedip-seq-analysis-pipeline

Post-processing pipeline for next-generation circulating methylome data generated by cfMeDIP-seq

cfmedip_analysis

Pre-processing pipeline to transform MEDIPS output wig files into matrix of chromosomal bins by samples

clump

cnaqc

CNAqc - Copy Number Alteration (CNA) Quality Check package

consensuscruncher

ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.

crescent

The CanceR Single Cell ExpressioN Toolkit one-line-command applications.

crescent-frontend

CReSCENT Portal: https://crescent.cloud | CReSCENT Docs: https://pughlab.github.io/crescent-frontend/

ctims

CTIMS project

ctims-pages

CTIMS Github Pages

data-processor

Script to convert from VCF files to MAF files ready to be imported into cBioPortal