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ats-motif-prediction

Python scripts that predict RBP binding motifs based on target site accessibility in bound (positive) and unbound (negative) transcripts.

cns-ball-discordance

Pipeline for using Pairtree to compare subclone distributions in acute lymphoblastic leukemias between CNS and bone marrow samples. Paper forthcoming.

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.

crc-dtp-ith-analysis

Pipeline for evaluating intratumor genetic heterogeneity in colorectal cancer patients. Used in paper at https://www.cell.com/cell/fulltext/S0092-8674(20)31535-X.

genometracksig

lmgraph

Algorithm to integrate network and attribute data for gene function prediction

mlworkshop

Machine learning workshop presented at GLBIO 2016

mtor-rcc

Analysis of TCGA/IMPACT datasets, and mTOR mutation status across cancer types

orchard

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.

pairtree-experiments

pan-code

pearsim

Framework for generating simulated data with which to evaluate cancer evolutionary history reconstruction methods. Suitable for use with Pairtree, SubMARine, and other methods.

phylosub

phylowgs

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

plos-medicine-joint-patterns

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

qapa

RNA-seq Quantification of Alternative Polyadenylation

rnacompete

Data analysis scripts for RNAcompete.

rnacompete-s

rnacompete_classifier

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

rnascan

Python package for scanning RNA sequences with sequence and structure PFMs

sbn

Generalizing Phylogenetic Posterior Estimator from MCMC samples via subplit Bayesian networks

smchet-challenge

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

spoilsport

submarine

Code for SubMARine.

submarine_data

Simulated data SubMARine was evaluated on.

tracksig

A framework to infer mutational signatures in cancer over time

tracksigfreq

R package for TrackSig and TrackSigFreq

weme

Weighted Median subclonal consensus method