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    31 repositories

    • splikit

      Public
      Splikit /ˈsplaɪ.kɪt/ is a toolkit designed for analyzing high-dimensional single-cell splicing data.
      rna-splicingsingle-cell-ge
      rna-splicingsingle-cell-ge
      R
      •
      Other
      •0•1•0•0•Updated Apr 24, 2026Apr 24, 2026

    • MAGIX

      Public
      MAGIX: Model-based Analysis of Genomic Intervals with eXponential enrichment.
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 10, 2026Apr 10, 2026

    • sclsd

      Public
      scLSD: A Latent Space Thermodynamic Model of Cell Differentiation
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • gedi2

      Public
      A high-performance R package for single-cell genomics
      single-cell-genomicssingle-cell-rna-seqhuman-cell-atlas
      single-cell-genomicssingle-cell-rna-seqhuman-cell-atlas
      R
      •
      Other
      •0•2•0•0•Updated Feb 22, 2026Feb 22, 2026

    • gedi2_manuscript

      Public
      Reproducible Code for the gedi2 Manuscript
      R
      •0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • GEDI

      Public
      Gene Expression Decomposition and Integration
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•19•1•0•Updated Feb 9, 2026Feb 9, 2026

    • gedi2py

      Public
      A high-performance Python package for single-cell genomics
      experimentalpipsinglecellgenomics
      experimentalpipsinglecellgenomicsscverse
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 29, 2026Jan 29, 2026

    • sclsd-manuscript

      Public
      Notebooks for reproducing manuscript figures and analyses.
      Jupyter Notebook
      •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • mach-1-manuscript

      Public
      Pre-/Post-Mach-1 Analyses Scripts and Notebooks
      R
      •
      MIT License
      •1•0•1•0•Updated Oct 3, 2025Oct 3, 2025

    • mach-1.5-prep

      Public
      Scripts to download, preprocess, and compress NCBI RefSeq annotations and genomes for training Mach-1.5 models.
      R
      •0•0•0•0•Updated Jul 15, 2025Jul 15, 2025

    • MPAQT

      Public
      Shell
      •
      MIT License
      •0•7•0•0•Updated May 28, 2025May 28, 2025

    • 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

    • 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•1•0•0•Updated Jul 10, 2024Jul 10, 2024

    • trex_manuscript

      Public
      Jupyter Notebook
      •0•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•14•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-se…
      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
      •2•9•2•1•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
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