morrislab/metient

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morrislab/metient

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phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.

TrackSig

A framework to infer mutational signatures in cancer over time

qapa

RNA-seq Quantification of Alternative Polyadenylation

pairtree

Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.

mlworkshop

Machine learning workshop presented at GLBIO 2016

Jupyter Notebook

phylosub

submarine

Code for SubMARine.

RNAcompete

Data analysis scripts for RNAcompete.

rnascan

Python package for scanning RNA sequences with sequence and structure PFMs

TrackSigFreq

R package for TrackSig and TrackSigFreq

orchard

GenomeTrackSig

damuta

Tandem signatures of DNA damage and misrepair in cancer

smchet-challenge

Data related to the ICGC-TCGA DREAM Somatic Mutation Calling - Tumour Heterogeneity Challenge.

consensus-bp

Pipeline for creating consensus copy-number aberration (CNA) segmentation (breakpoints) for ICGC Pan Cancer Analysis of Whole Genomes project. Used in paper at https://www.biorxiv.org/content/10.1101/312041v5.

submarine_data

Simulated data SubMARine was evaluated on.

plos-medicine-joint-patterns

Source code for the juvenile idiopathic arthritis joint patterns paper published in PLOS Medicine, 2019.

PAN-cODE

Jupyter Notebook

RNAcompete_classifier

This repository contains the code and data for training the RNAcompete experiment classifier used in Ray et al. 2022

weme

Weighted Median subclonal consensus method