Stars
Reference data: BED files, genes, transcripts, variations.
Documents from a live coding session by Christopher Wolfram related to content from the 2016 film Arrival
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
ASCETIC (Agony-baSed Cancer EvoluTion InferenCe) is a novel framework for the inference of a set of statistically significant temporal patterns involving alternations in driver genes from cancer ge…
heiniglab / DeepSom
Forked from sergeyvilov/DeepSomA CNN - based pipeline for calling somatic SNP and INDEL variants without a matched normal
Somatic copy number analysis using WGS paired end wholegenome sequencing
Battenberg R package for subclonal copynumber estimation
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Create timecourse "fish plots" that show changes in the clonal architecture of tumors
Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data
Model-based tumour subclonal deconvolution using population genetics
Official code repository for GATK versions 4 and up
An R package to plot maps of clone distributions in somatic evolution
The analysis repository for the Open Pediatric Brain Tumor Atlas Project
Shows how to use Shiny to demo your machine learning model or to submit Machine Learning Challenges.
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities i…
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE