Pinned Repositories
mlworkshop
Machine learning workshop presented at GLBIO 2016
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.
phylosub
phylowgs
Application for inferring subclonal composition and evolution from whole-genome sequencing data.
qapa
RNA-seq Quantification of Alternative Polyadenylation
RNAcompete
Data analysis scripts for RNAcompete.
rnascan
Python package for scanning RNA sequences with sequence and structure PFMs
submarine
Code for SubMARine.
TrackSig
A framework to infer mutational signatures in cancer over time
TrackSigFreq
R package for TrackSig and TrackSigFreq
Morris Lab's Repositories
morrislab/phylowgs
Application for inferring subclonal composition and evolution from whole-genome sequencing data.
morrislab/TrackSig
A framework to infer mutational signatures in cancer over time
morrislab/qapa
RNA-seq Quantification of Alternative Polyadenylation
morrislab/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.
morrislab/mlworkshop
Machine learning workshop presented at GLBIO 2016
morrislab/phylosub
morrislab/submarine
Code for SubMARine.
morrislab/RNAcompete
Data analysis scripts for RNAcompete.
morrislab/rnascan
Python package for scanning RNA sequences with sequence and structure PFMs
morrislab/TrackSigFreq
R package for TrackSig and TrackSigFreq
morrislab/metient
morrislab/orchard
morrislab/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.
morrislab/GenomeTrackSig
morrislab/smchet-challenge
Data related to the ICGC-TCGA DREAM Somatic Mutation Calling - Tumour Heterogeneity Challenge.
morrislab/PAN-cODE
morrislab/plos-medicine-joint-patterns
Source code for the juvenile idiopathic arthritis joint patterns paper published in PLOS Medicine, 2019.
morrislab/RNAcompete_classifier
This repository contains the code and data for training the RNAcompete experiment classifier used in Ray et al. 2022
morrislab/submarine_data
Simulated data SubMARine was evaluated on.
morrislab/weme
Weighted Median subclonal consensus method
morrislab/ATS-motif-prediction
Python scripts that predict RBP binding motifs based on target site accessibility in bound (positive) and unbound (negative) transcripts.
morrislab/cns-ball-discordance
Pipeline for using Pairtree to compare subclone distributions in acute lymphoblastic leukemias between CNS and bone marrow samples. Paper forthcoming.
morrislab/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.
morrislab/lmgraph
Algorithm to integrate network and attribute data for gene function prediction
morrislab/pearsim
Framework for generating simulated data with which to evaluate cancer evolutionary history reconstruction methods. Suitable for use with Pairtree, SubMARine, and other methods.
morrislab/RNAcompete-S
morrislab/SpoilSport
morrislab/mtor-rcc
Analysis of TCGA/IMPACT datasets, and mTOR mutation status across cancer types
morrislab/pairtree-experiments
morrislab/sbn
Generalizing Phylogenetic Posterior Estimator from MCMC samples via subplit Bayesian networks