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    35 repositories

    • metient

      Public
      Jupyter Notebook
      •
      MIT License
      •2•11•0•0•Updated Apr 2, 2026Apr 2, 2026

    • mRNABench

      Public
      Collection of mRNA benchmarks
      Python
      •
      GNU Affero General Public License v3.0
      •3•49•0•0•Updated Mar 25, 2026Mar 25, 2026

    • qapa

      Public
      RNA-seq Quantification of Alternative Polyadenylation
      Python
      •
      GNU General Public License v3.0
      •10•53•0•0•Updated Mar 21, 2026Mar 21, 2026

    • jple

      Public
      Joint Protein-Ligand Embedding
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Oct 3, 2025Oct 3, 2025

    • RNAcompete-deprecated

      Public archive
      Data analysis scripts for RNAcompete.
      Perl
      •
      MIT License
      •4•10•0•0•Updated Oct 1, 2025Oct 1, 2025

    • rnacompete

      Public
      Reproducible pipeline to process and summarize RNAcompete data.
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Oct 1, 2025Oct 1, 2025

    • RBPbinding

      Public archive
      Code for "A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function"
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Oct 1, 2025Oct 1, 2025

    • damuta

      Public
      Tandem signatures of DNA damage and misrepair in cancer
      Python
      •
      Other
      •0•6•1•0•Updated Sep 12, 2025Sep 12, 2025

    • orchard

      Public
      Python
      •
      MIT License
      •1•6•0•0•Updated Jan 28, 2025Jan 28, 2025

    • pairtree

      Public
      Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on …
      Python
      •
      MIT License
      •10•44•0•0•Updated Apr 18, 2024Apr 18, 2024

    • GenomeTrackSig

      Public
      R
      •
      MIT License
      •0•4•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
      •56•115•61•4•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, an…
      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-…
      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•6•1•0•Updated Oct 24, 2019Oct 24, 2019

    • TrackSig

      Public
      A framework to infer mutational signatures in cancer over time
      R
      •
      MIT License
      •17•58•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 …
      Python
      •
      MIT License
      •0•2•1•0•Updated Sep 4, 2018Sep 4, 2018
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