aertslab

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80 repositories

scatac_fragment_tools
Public
Tools for working with scATAC-seq fragment files
fragments fragment single-cell
fragments fragment single-cell scatac-seq
Python
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MIT License
•0•7•0•0•Updated Feb 25, 2026Feb 25, 2026
pycisTopic
Public
pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
Jupyter Notebook
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Other
•17•78•58•5•Updated Feb 25, 2026Feb 25, 2026
TF-MINDI
Public
Transcription Factor Motif Instance Neighborhood Decomposition and Interpretation
Python
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Other
•2•14•2•4•Updated Feb 24, 2026Feb 24, 2026
CREsted
Public
CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specifi…
deep-learning sequence-models single-cell-genomics
deep-learning sequence-models single-cell-genomics scatac-seq regulatory-genomics scverse
Python
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Other
•9•57•7•3•Updated Feb 20, 2026Feb 20, 2026
single_cell_toolkit
Public
Tools for correcting single cell barcodes for various scATAC-seq techniques and creating fragment files and spltting BAM files per cluster.
scatac-seq hydrop
scatac-seq hydrop
Shell
•4•29•3•0•Updated Feb 16, 2026Feb 16, 2026
ctxcore
Public
Core functions for pycisTarget and the SCENIC tool suite
Python
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GNU General Public License v3.0
•8•5•2•2•Updated Jan 30, 2026Jan 30, 2026
scenicplus
Public
SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromati…
Jupyter Notebook
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Other
•52•246•191•9•Updated Jan 16, 2026Jan 16, 2026
GAME-DeepBICCN2-Predictor
Public
DeepBICCN2 Cell Type-Specific Chromatin Accessibility Predictor Container for the Genomic API for Model Evaluation (GAME)
Python
•0•0•0•0•Updated Jan 8, 2026Jan 8, 2026
GAME-BICCN-Evaluator-EnhancerLabel
Public
GAME container files for the BICCN evaluator (on-target enhancer cell type classification)
Python
•0•0•0•0•Updated Jan 8, 2026Jan 8, 2026
SCope
Public
Fast visualization tool for large-scale and high dimensional single-cell data
aws cloud reactjs
aws cloud reactjs grpc gene-expression single-cell loom large-scale-data-visualization gene-regulatory-network
Python
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GNU General Public License v3.0
•15•78•98•4•Updated Dec 16, 2025Dec 16, 2025
CREsted-paper
Public
Jupyter Notebook
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MIT License
•0•2•0•0•Updated Dec 3, 2025Dec 3, 2025
HyDrop_v2_paper
Public
To facilitate the cost-effective generation of large scATAC-seq atlases for deep learning model training, we developed a new version of the open-source microflu…
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Nov 10, 2025Nov 10, 2025
PUMATAC
Public
Pipeline for Universal Mapping of ATAC-seq
pipeline nextflow sequencing
pipeline nextflow sequencing atac-seq chromatin
Nextflow
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GNU General Public License v2.0
•1•25•1•0•Updated Sep 23, 2025Sep 23, 2025
pySCENIC
Public
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to …
transcription-factors transcriptomics single-cell
transcription-factors transcriptomics single-cell gene-regulatory-network
Python
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GNU General Public License v3.0
•203•580•233•5•Updated Jun 26, 2025Jun 26, 2025
scenicplus_core
Public
Collection of common algorithms and functions for all SCENIC+ related tools.
Rust
•0•0•0•0•Updated Jun 20, 2025Jun 20, 2025
create_cisTarget_databases
Public
Create cisTarget databases
Python
•7•56•38•0•Updated Jun 18, 2025Jun 18, 2025
mango-ingest
Public
Python
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BSD 3-Clause "New" or "Revised" License
•2•0•0•0•Updated Jun 12, 2025Jun 12, 2025
Nova-ST
Public
A repository containing the analysis scripts for Nova-ST data
Jupyter Notebook
•0•9•1•0•Updated Apr 3, 2025Apr 3, 2025
DeepBrain
Public
DeepBrain: a collection of vertebrate sequence-based enhancer models aimed at understanding brain cell type enhancer code across and within species
genomics evolution deeplearning
genomics evolution deeplearning enhancer single-cell brain
Jupyter Notebook
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Other
•0•8•0•0•Updated Jan 30, 2025Jan 30, 2025
pycistarget
Public
pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.
Python
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Other
•4•18•16•0•Updated Jan 21, 2025Jan 21, 2025
regulatory_regions_delineation
Public
Create regulatory regions delineation
Python
•0•1•0•0•Updated Nov 15, 2024Nov 15, 2024
PUMATAC_tutorial
Public
Jupyter Notebook
•2•8•0•0•Updated Oct 6, 2024Oct 6, 2024
scforest
Public
scforest: a visual overview of single cell technology
TeX
•1•4•0•0•Updated Aug 30, 2024Aug 30, 2024
biopython
Public
Official git repository for Biopython (converted from CVS)
Python
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Other
•1.9k•0•0•0•Updated Aug 12, 2024Aug 12, 2024
nextcloud_share_url_downloader
Public
Download files from and list content of NextCloud (password protected) share directly from the command line without needing a webbrowser.
Shell
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MIT License
•11•27•3•0•Updated Jun 18, 2024Jun 18, 2024
SpatialNF
Public
Spatial transcriptomics NextFlow pipelines
Python
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GNU General Public License v3.0
•2•6•1•0•Updated May 16, 2024May 16, 2024
SCENIC
Public
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
HTML
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GNU General Public License v3.0
•97•477•112•1•Updated Apr 5, 2024Apr 5, 2024
arboreto
Public
A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
python machine-learning scalable
python machine-learning scalable random-forest network inference gene-regulation ensemble-learning dask gradient-boosting
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•35•66•28•2•Updated Apr 5, 2024Apr 5, 2024
cisTopic
Public
cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
HTML
•27•144•7•0•Updated Apr 5, 2024Apr 5, 2024
AUCell
Public
AUCell: score single cells with gene regulatory networks
R
•30•187•20•2•Updated Mar 9, 2024Mar 9, 2024