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    24 repositories

    • lorna-manuscript

      Public
      LoRNA-SH: A long-context RNA foundation model for predicting transcriptome architecture. Pre-processing and downstream analysis scripts.
      R
      •
      MIT License
      •1•4•0•0•Updated Dec 6, 2024Dec 6, 2024

    • MAGIX

      Public
      MAGIX: Model-based Analysis of Genomic Intervals with eXponential enrichment.
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • RCADEEM

      Public
      Recognition Code-Assisted Discovery of regulatory Elements by Expectation Maximization
      C
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

    • GEDI

      Public
      Gene Expression Decomposition and Integration
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•16•0•0•Updated Aug 21, 2024Aug 21, 2024

    • MPAQT

      Public
      Shell
      •
      MIT License
      •0•7•0•0•Updated Aug 18, 2024Aug 18, 2024

    • trex

      Public
      TRex: a computational method to associate changes in exon-centric splicing events with experimental variables form complex experimental designs
      R
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Jul 10, 2024Jul 10, 2024

    • trex_manuscript

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Jul 10, 2024Jul 10, 2024

    • GEDI_manuscript

      Public
      This repository hosts R markdown notebooks reproducing the figures from the GEDI manuscript
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•0•1•0•Updated May 17, 2024May 17, 2024

    • DiffRAC

      Public
      A flexible R function for comparing response proportions in sequencing count data
      R
      •
      GNU General Public License v3.0
      •1•8•0•0•Updated May 13, 2024May 13, 2024

    • hgthesis_lms

      Public
      ALTERNATIVE SPLICING PROGRAMS IN TUMOR DEVELOPMENT AND PROGRESSION
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Feb 22, 2024Feb 22, 2024

    • REMBRANDTS

      Public
      REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability
      R
      •
      GNU General Public License v3.0
      •11•13•7•1•Updated Dec 16, 2023Dec 16, 2023

    • JAMS

      Public
      Quantitative modeling of sequence, DNA accessibility, and methylation preferences of transcription factors using ChIP-seq data.
      R
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Nov 1, 2023Nov 1, 2023

    • PhantomPurgeR

      Public
      R package for the optimal purging of phantom molecules by the robust estimation of the sample index hopping rate in multiplexed droplet-based single-cell RNA-seq data
      R
      •
      BSD 2-Clause "Simplified" License
      •1•3•0•0•Updated Jul 12, 2023Jul 12, 2023

    • JAMS_novo

      Public
      Quantitative modeling of sequence, DNA accessibility, and methylation preferences of transcription factors using ChIP-seq data.
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 26, 2022Oct 26, 2022

    • BETAS

      Public
      Bayesian Estimation of Transcript Abundance and Stability
      C++
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 19, 2022Sep 19, 2022

    • CRIES

      Public
      Counting Reads for Intronic and Exonic Segments
      R
      •
      GNU General Public License v3.0
      •1•7•2•0•Updated Sep 19, 2022Sep 19, 2022

    • transcriptional_reprogramming_muscle_cells

      Public
      Dynamics of niche mediated transcriptional reprogramming of muscle stem cells
      HTML
      •
      BSD 2-Clause "Simplified" License
      •1•1•0•0•Updated Mar 24, 2022Mar 24, 2022

    • Alkallas_et_al_2017

      Public
      0•0•0•0•Updated Mar 11, 2020Mar 11, 2020

    • Perron_et_al_2018

      Public
      R
      •0•0•0•0•Updated Mar 11, 2020Mar 11, 2020

    • phantom_purge

      Public
      Please go to https://github.com/csglab/PhantomPurgeR
      R
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Feb 29, 2020Feb 29, 2020

    • RCADE2

      Public
      Recognition Code-Assisted Discovery of regulatory Elements v2
      C++
      •
      GNU General Public License v2.0
      •1•5•0•1•Updated Apr 17, 2019Apr 17, 2019

    • share_UCSC

      Public
      Test: hosting bigwig files for UCSC
      0•0•0•0•Updated Feb 1, 2019Feb 1, 2019

    • RCADER

      Public
      Recognition Code-Assisted Discovery of regulatory Elements by Regression
      C++
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated May 17, 2018May 17, 2018

    • MoSBAT

      Public
      Motif Similarity Based on Affinity of Targets
      HTML
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Sep 29, 2016Sep 29, 2016