Skip to content

@csglab Computational and Statistical Genomics Lab

All

    Repositories list

    39 repositories

    • leaf-1-figures

      Public
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Oct 26, 2026Oct 26, 2026

    • sclsd-manuscript

      Public
      Notebooks for reproducing manuscript figures and analyses.
      Jupyter Notebook
      •0•0•0•0•Updated Oct 23, 2026Oct 23, 2026

    • sclsd

      Public
      scLSD: A Latent Space Thermodynamic Model of Cell Differentiation
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 23, 2026Oct 23, 2026

    • scConvexNMF

      Public
      Single cell convex non-negative matrix factorization
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•2•0•0•Updated Oct 9, 2026Oct 9, 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
      •1•22•0•0•Updated Oct 5, 2026Oct 5, 2026

    • MPAQT

      Public
      Multi-Platform Aggregation and Quantification of Transcripts
      R
      •
      Other
      •0•1•0•0•Updated Oct 1, 2026Oct 1, 2026

    • RBP-miRNA-manuscript

      Public
      R project and notebooks required to reproduce the analyses, figures, and tables presented in the publication: A map of RBP-miRNA regulatory connections for deci…
      HTML
      •
      Other
      •0•0•0•0•Updated Sep 28, 2026Sep 28, 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 Aug 18, 2026Aug 18, 2026

    • RCADEEM

      Public
      Recognition Code-Assisted Discovery of regulatory Elements by Expectation Maximization
      C
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 18, 2026Aug 18, 2026

    • splikit

      Public
      Splikit /ˈsplaɪ.kɪt/ is a toolkit designed for analyzing high-dimensional single-cell splicing data.
      cranrna-splicingsingle-cell-ge
      cranrna-splicingsingle-cell-ge
      R
      •
      Other
      •0•2•1•0•Updated Jul 30, 2026Jul 30, 2026

    • leaf-1

      Public
      Python
      •
      Other
      •1•3•0•0•Updated Jul 9, 2026Jul 9, 2026

    • RCC_manuscript

      Public
      This repository hosts notebooks reproducing the figures from the RCC manuscript
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jun 18, 2026Jun 18, 2026

    • robustness_ms

      Public
      Source code for "Recursive mutational robustness in cancer through intra- and intergenic compensation"
      Python
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • intom

      Public
      intom⿻Perturbational robustness estimation using integrative omics data
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 11, 2026Jun 11, 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•21•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•2•0•0•Updated Jan 29, 2026Jan 29, 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_legacy

      Public
      Shell
      •
      MIT License
      •0•8•0•0•Updated May 28, 2025May 28, 2025

    • 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•15•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
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.