somatic-variants topic

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 in e...

AlexandrovLab

Bayesian haplotype-based mutation calling

luntergroup

🌲 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

ShixiangWang

An ensemble approach to accurately detect somatic mutations using SomaticSeq

bioinform

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

bioinform

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file)....

AlexandrovLab

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

PoisonAlien

highly-efficient & lightweight mutation signature matrix aggregation

carjed

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

KarchinLab

R wrapper for utilizing the SigProfilerMatrixGenerator framework

AlexandrovLab