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    28 repositories

    • hemberg-lab.github.io

      Public
      SCSS
      •
      MIT License
      •2•0•0•0•Updated May 2, 2026May 2, 2026

    • tigit-paper-figures

      Public
      R
      •0•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • MicroExonator

      Public
      Snakemake pipeline for microexon discovery and quantification
      Python
      •8•21•9•1•Updated Jan 16, 2025Jan 16, 2025

    • scASfind

      Public
      Identification of cell type-specific alternative splicing events using scASfind
      HTML
      •
      Other
      •0•11•2•0•Updated Mar 23, 2024Mar 23, 2024

    • scfind

      Public
      R
      •
      GNU General Public License v3.0
      •9•43•0•0•Updated Oct 20, 2023Oct 20, 2023

    • scfindME

      Public
      scfindME adaps scfind to alternative splicing analysis
      Jupyter Notebook
      •
      MIT License
      •0•6•0•0•Updated Apr 16, 2023Apr 16, 2023

    • sc3s

      Public
      Single Cell Consensus Clustering with Speed
      Python
      •
      GNU General Public License v3.0
      •6•23•3•0•Updated Dec 12, 2022Dec 12, 2022

    • scRNA.seq.course

      Public
      Analysis of single cell RNA-seq data course
      rcoursesequencing
      rcoursesequencingbookdownscrna-seqscrna-seq-analysis
      TeX
      •
      GNU General Public License v3.0
      •1.3k•679•18•5•Updated Apr 11, 2022Apr 11, 2022

    • Georgakopoulos_Soares_and_Parada_2022

      Public
      HTML
      •0•0•0•0•Updated Mar 3, 2022Mar 3, 2022

    • VASAseq_2022

      Public
      This repository aims to serve as an index of the work described at Salmen & De Jonghe et. al 2022
      HTML
      •9•25•0•0•Updated Feb 21, 2022Feb 21, 2022

    • SC3

      Public
      A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
      single-cell-rna-seqbioconductor-packagehuman-cell-atlas
      single-cell-rna-seqbioconductor-packagehuman-cell-atlas
      R
      •
      GNU General Public License v3.0
      •55•129•17•2•Updated Jun 28, 2021Jun 28, 2021

    • RNA_seq_snakepipes

      Public
      HTML
      •9•6•0•0•Updated Jun 9, 2021Jun 9, 2021

    • yeastDrop-Seq

      Public
      Computational pipeline to reproduce the results in the paper.
      R
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated May 14, 2021May 14, 2021

    • scRNA.seq.datasets

      Public
      Collection of public scRNA-Seq datasets used by our group
      dockerjenkinsaws
      dockerjenkinsawsopenstackmkdocsdatasets3-storagesingle-cell
      R
      •
      GNU General Public License v3.0
      •59•171•6•7•Updated May 4, 2021May 4, 2021

    • scfind-paper-figures

      Public
      Scripts to recreate figures from the scfind paper
      Julia
      •
      GNU General Public License v3.0
      •3•6•0•0•Updated Jan 19, 2021Jan 19, 2021

    • scmap-shiny

      Public
      HTML
      •
      GNU General Public License v3.0
      •4•8•0•0•Updated Nov 24, 2020Nov 24, 2020

    • scmap

      Public
      A tool for unsupervised projection of single cell RNA-seq data
      rprojection-mappingsingle-cell-rna-seq
      rprojection-mappingsingle-cell-rna-seqbioconductor-packagehuman-cell-atlas
      R
      •
      GNU General Public License v3.0
      •11•100•20•1•Updated Nov 24, 2020Nov 24, 2020

    • scfind-shiny

      Public
      HTML
      •
      GNU General Public License v3.0
      •4•2•0•0•Updated Aug 11, 2020Aug 11, 2020

    • sctransfermap

      Public
      prediction of cell type from single-cell data
      R
      •1•0•0•0•Updated Nov 8, 2019Nov 8, 2019

    • SnakePool

      Public
      Python
      •0•0•0•0•Updated Mar 29, 2019Mar 29, 2019

    • D3E

      Public
      Discrete Distributional Differential Expression
      differential-expressionsingle-cell-rna-seqhuman-cell-atlas
      differential-expressionsingle-cell-rna-seqhuman-cell-atlas
      Python
      •
      GNU General Public License v3.0
      •9•23•3•0•Updated Jan 3, 2019Jan 3, 2019

    • nrg-paper-figures

      Public
      R
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Nov 15, 2018Nov 15, 2018

    • scmap-paper-figures

      Public
      Scripts to recreate figures from the scmap paper
      R
      •
      GNU Lesser General Public License v3.0
      •4•5•1•0•Updated Mar 13, 2018Mar 13, 2018

    • tutorials

      Public
      HTML
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Dec 5, 2017Dec 5, 2017

    • SC3-paper-figures

      Public
      Scripts to recreate figures from the SC3 paper
      R
      •
      GNU General Public License v3.0
      •16•41•0•0•Updated Mar 1, 2017Mar 1, 2017

    • FastSC3

      Public
      A tool for fast unsupervised clustering of very large single cell RNA-Seq data
      R
      •0•4•0•0•Updated Dec 12, 2016Dec 12, 2016

    • scRNA.seq.funcs

      Public
      R package containing our own functions used in the scRNA.seq.course
      R
      •2•3•1•0•Updated Jun 20, 2016Jun 20, 2016

    • MPRAnator

      Public
      A webtool to create DNA sequence variants
      Python
      •1•1•0•0•Updated Dec 27, 2015Dec 27, 2015
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