Hemberg Lab

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28 repositories

hemberg-lab.github.io
Public
SCSS
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MIT License
•2•0•0•0•Updated Dec 26, 2025Dec 26, 2025
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•20•9•1•Updated Jan 16, 2025Jan 16, 2025
scASfind
Public
Identification of cell type-specific alternative splicing events using scASfind
HTML
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Other
•0•10•2•0•Updated Mar 23, 2024Mar 23, 2024
scfind
Public
R
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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
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MIT License
•0•6•0•0•Updated Apr 16, 2023Apr 16, 2023
sc3s
Public
Single Cell Consensus Clustering with Speed
Python
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GNU General Public License v3.0
•6•21•3•0•Updated Dec 12, 2022Dec 12, 2022
scRNA.seq.course
Public
Analysis of single cell RNA-seq data course
r course sequencing
r course sequencing bookdown scrna-seq scrna-seq-analysis
TeX
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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•24•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-seq bioconductor-package human-cell-atlas
single-cell-rna-seq bioconductor-package human-cell-atlas
R
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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
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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
docker jenkins aws
docker jenkins aws openstack mkdocs dataset s3-storage single-cell
R
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GNU General Public License v3.0
•59•173•6•7•Updated May 4, 2021May 4, 2021
scfind-paper-figures
Public
Scripts to recreate figures from the scfind paper
Julia
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GNU General Public License v3.0
•3•6•0•0•Updated Jan 19, 2021Jan 19, 2021
scmap-shiny
Public
HTML
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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
r projection-mapping single-cell-rna-seq
r projection-mapping single-cell-rna-seq bioconductor-package human-cell-atlas
R
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GNU General Public License v3.0
•11•97•20•1•Updated Nov 24, 2020Nov 24, 2020
scfind-shiny
Public
HTML
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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-expression single-cell-rna-seq human-cell-atlas
differential-expression single-cell-rna-seq human-cell-atlas
Python
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GNU General Public License v3.0
•9•22•3•0•Updated Jan 3, 2019Jan 3, 2019
nrg-paper-figures
Public
R
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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
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GNU Lesser General Public License v3.0
•4•5•1•0•Updated Mar 13, 2018Mar 13, 2018
tutorials
Public
HTML
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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
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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•3•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