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    30 repositories

    • orchard

      Public
      Python
      •
      MIT License
      •1•4•0•0•Updated Nov 26, 2024Nov 26, 2024

    • metient

      Public
      Jupyter Notebook
      •1•5•1•0•Updated Sep 25, 2024Sep 25, 2024

    • pairtree

      Public
      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.
      Python
      •
      MIT License
      •11•37•0•1•Updated Apr 18, 2024Apr 18, 2024

    • qapa

      Public
      RNA-seq Quantification of Alternative Polyadenylation
      Python
      •
      GNU General Public License v3.0
      •10•44•4•0•Updated Jun 16, 2023Jun 16, 2023

    • GenomeTrackSig

      Public
      R
      •
      MIT License
      •0•3•0•0•Updated May 5, 2023May 5, 2023

    • TrackSigFreq

      Public
      R package for TrackSig and TrackSigFreq
      R
      •
      MIT License
      •0•5•2•0•Updated Oct 31, 2022Oct 31, 2022

    • RNAcompete_classifier

      Public
      This repository contains the code and data for training the RNAcompete experiment classifier used in Ray et al. 2022
      Python
      •0•1•0•0•Updated Oct 28, 2022Oct 28, 2022

    • phylowgs

      Public
      Application for inferring subclonal composition and evolution from whole-genome sequencing data.
      Python
      •
      GNU General Public License v3.0
      •55•108•60•5•Updated Oct 12, 2022Oct 12, 2022

    • PAN-cODE

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Jul 20, 2022Jul 20, 2022

    • mtor-rcc

      Public
      Analysis of TCGA/IMPACT datasets, and mTOR mutation status across cancer types
      R
      •1•0•0•0•Updated Apr 19, 2022Apr 19, 2022

    • submarine

      Public
      Code for SubMARine.
      Python
      •
      GNU General Public License v3.0
      •1•8•1•0•Updated May 28, 2021May 28, 2021

    • pearsim

      Public
      Framework for generating simulated data with which to evaluate cancer evolutionary history reconstruction methods. Suitable for use with Pairtree, SubMARine, and other methods.
      Python
      •1•0•0•0•Updated Apr 28, 2021Apr 28, 2021

    • cns-ball-discordance

      Public
      Pipeline for using Pairtree to compare subclone distributions in acute lymphoblastic leukemias between CNS and bone marrow samples. Paper forthcoming.
      Python
      •0•0•0•0•Updated Feb 22, 2021Feb 22, 2021

    • pairtree-experiments

      Public
      0•0•0•0•Updated Dec 17, 2020Dec 17, 2020

    • submarine_data

      Public
      Simulated data SubMARine was evaluated on.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Oct 6, 2020Oct 6, 2020

    • crc-dtp-ith-analysis

      Public
      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.
      Shell
      •0•0•0•0•Updated Aug 14, 2020Aug 14, 2020

    • sbn

      Public
      Generalizing Phylogenetic Posterior Estimator from MCMC samples via subplit Bayesian networks
      Jupyter Notebook
      •7•0•0•0•Updated Jan 14, 2020Jan 14, 2020

    • smchet-challenge

      Public
      Data related to the ICGC-TCGA DREAM Somatic Mutation Calling - Tumour Heterogeneity Challenge.
      Python
      •4•2•1•1•Updated Nov 15, 2019Nov 15, 2019

    • rnascan

      Public
      Python package for scanning RNA sequences with sequence and structure PFMs
      Python
      •
      GNU Affero General Public License v3.0
      •1•5•1•0•Updated Oct 24, 2019Oct 24, 2019

    • TrackSig

      Public
      A framework to infer mutational signatures in cancer over time
      R
      •
      MIT License
      •17•53•4•1•Updated Jul 9, 2019Jul 9, 2019

    • plos-medicine-joint-patterns

      Public
      Source code for the juvenile idiopathic arthritis joint patterns paper published in PLOS Medicine, 2019.
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 18, 2019Jan 18, 2019

    • weme

      Public
      Weighted Median subclonal consensus method
      R
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Dec 27, 2018Dec 27, 2018

    • SpoilSport

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 27, 2018Dec 27, 2018

    • consensus-bp

      Public
      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.
      Python
      •
      MIT License
      •0•2•1•0•Updated Sep 4, 2018Sep 4, 2018

    • RNAcompete

      Public
      Data analysis scripts for RNAcompete.
      Perl
      •
      MIT License
      •3•8•0•0•Updated Aug 29, 2018Aug 29, 2018

    • ATS-motif-prediction

      Public
      Python scripts that predict RBP binding motifs based on target site accessibility in bound (positive) and unbound (negative) transcripts.
      Python
      •
      MIT License
      •1•0•1•0•Updated May 18, 2017May 18, 2017

    • RNAcompete-S

      Public
      Perl
      •0•0•0•0•Updated Mar 15, 2017Mar 15, 2017

    • lmgraph

      Public
      Algorithm to integrate network and attribute data for gene function prediction
      Python
      •0•0•0•0•Updated Feb 11, 2017Feb 11, 2017

    • mlworkshop

      Public
      Machine learning workshop presented at GLBIO 2016
      Jupyter Notebook
      •2•11•0•0•Updated May 17, 2016May 17, 2016

    • phylosub

      Public
      Python
      •11•10•5•1•Updated Jul 6, 2015Jul 6, 2015