Morris Lab's repositories
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
RNAcompete
Data analysis scripts for RNAcompete.
TrackSigFreq
R package for TrackSig and TrackSigFreq
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.
smchet-challenge
Data related to the ICGC-TCGA DREAM Somatic Mutation Calling - Tumour Heterogeneity Challenge.
plos-medicine-joint-patterns
Source code for the juvenile idiopathic arthritis joint patterns paper published in PLOS Medicine, 2019.
RNAcompete_classifier
This repository contains the code and data for training the RNAcompete experiment classifier used in Ray et al. 2022
submarine_data
Simulated data SubMARine was evaluated on.
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.
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.