Repositories list

• 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-specific sequences.

  deep-learningsequence-modelssingle-cell-genomics+ 3scatac-seqregulatory-genomicsscverse

  Python

  •

  Other

  •3•28•2•5•Updated Jan 8, 2025Jan 8, 2025

• 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-seqhydrop

  Shell

  •3•26•2•0•Updated Jan 6, 2025Jan 6, 2025

• pycisTopic

  Public
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

  Jupyter Notebook

  •

  Other

  •13•59•48•2•Updated Dec 17, 2024Dec 17, 2024

• 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 chromatin accessibility (scATAC-seq) data.

  Jupyter Notebook

  •

  Other

  •32•193•128•4•Updated Dec 16, 2024Dec 16, 2024

• regulatory_regions_delineation

  Public
  Create regulatory regions delineation

  Python

  •0•1•0•0•Updated Nov 15, 2024Nov 15, 2024

• scatac_fragment_tools

  Public
  Tools for working with scATAC-seq fragment files

  fragmentsfragmentsingle-cell+ 1scatac-seq

  Python

  •0•6•0•0•Updated Nov 13, 2024Nov 13, 2024

• PUMATAC_tutorial

  Public
  Jupyter Notebook

  •1•7•0•0•Updated Oct 6, 2024Oct 6, 2024

• scforest

  Public
  scforest: a visual overview of single cell technology

  TeX

  •0•3•0•0•Updated Aug 30, 2024Aug 30, 2024

• biopython

  Public
  Official git repository for Biopython (converted from CVS)

  Python

  •

  Other

  •1.8k•0•0•0•Updated Aug 12, 2024Aug 12, 2024

• Nova-ST

  Public
  A repository containing the analysis scripts for Nova-ST data

  Jupyter Notebook

  •0•9•0•0•Updated Jul 1, 2024Jul 1, 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

  •

  MIT License

  •11•23•3•1•Updated Jun 18, 2024Jun 18, 2024

• SpatialNF

  Public
  Spatial transcriptomics NextFlow pipelines

  Python

  •

  GNU General Public License v3.0

  •0•2•1•0•Updated May 16, 2024May 16, 2024

• PUMATAC

  Public
  Pipeline for Universal Mapping of ATAC-seq

  pipelinenextflowsequencing+ 2atac-seqchromatin

  Nextflow

  •

  Other

  •1•24•1•0•Updated Apr 30, 2024Apr 30, 2024

• 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

  •

  Other

  •4•15•14•0•Updated Apr 23, 2024Apr 23, 2024

• DeepBrain

  Public
  DeepBrain: a collection of vertebrate sequence-based enhancer models aimed at understanding brain cell type enhancer code across and within species

  genomicsevolutiondeeplearning+ 3enhancersingle-cellbrain

  Jupyter Notebook

  •

  Other

  •0•5•0•0•Updated Apr 18, 2024Apr 18, 2024

• pySCENIC

  Public
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

  transcription-factorstranscriptomicssingle-cell+ 1gene-regulatory-network

  Python

  •

  GNU General Public License v3.0

  •186•462•203•3•Updated Apr 8, 2024Apr 8, 2024

• SCENIC

  Public
  SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

  HTML

  •

  GNU General Public License v3.0

  •95•428•106•1•Updated Apr 5, 2024Apr 5, 2024

• arboreto

  Public
  A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.

  pythonmachine-learningscalable+ 7random-forestnetworkinferencegene-regulationensemble-learningdaskgradient-boosting

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •26•54•28•1•Updated Apr 5, 2024Apr 5, 2024

• cisTopic

  Public
  cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data

  HTML

  •29•135•7•0•Updated Apr 5, 2024Apr 5, 2024

• ctxcore

  Public
  Core functions for pycisTarget and the SCENIC tool suite

  Python

  •

  GNU General Public License v3.0

  •7•3•2•1•Updated Mar 29, 2024Mar 29, 2024

• AUCell

  Public
  AUCell: score single cells with gene regulatory networks

  R

  •28•136•15•1•Updated Mar 9, 2024Mar 9, 2024

• RcisTarget

  Public
  RcisTarget: Transcription factor binding motif enrichment

  r-package

  HTML

  •9•36•13•0•Updated Mar 4, 2024Mar 4, 2024

• shap

  Public
  A game theoretic approach to explain the output of any machine learning model.

  Jupyter Notebook

  •

  MIT License

  •3.3k•0•0•0•Updated Jan 22, 2024Jan 22, 2024

• scATAC-seq_benchmark

  Public
  Jupyter Notebook

  •2•16•1•0•Updated Dec 15, 2023Dec 15, 2023

• scenicplus_analyses

  Public
  SCENIC+ analyses

  Jupyter Notebook

  •1•10•2•0•Updated Sep 26, 2023Sep 26, 2023

• spatial_fly_website

  Public
  CSS

  •0•0•1•0•Updated Sep 6, 2023Sep 6, 2023

• MendelCraft

  Public
  The MendelCraft mod, introducing Mendelian genetics to the chickens of Minecraft!

  Java

  •

  MIT License

  •1•5•3•0•Updated Aug 2, 2023Aug 2, 2023

• Bravo_et_al_Liver

  Public
  Bravo_et_al_Liver

  Jupyter Notebook

  •0•6•0•0•Updated Jul 16, 2023Jul 16, 2023

• LoomXpy

  Public
  Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulons

  Python

  •

  MIT License

  •3•6•1•0•Updated Jun 13, 2023Jun 13, 2023

• FlyBrain_website

  Public
  R

  •0•0•1•0•Updated May 8, 2023May 8, 2023