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Repository Details
Decoding gene regulation in the fly brain
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SCENIC
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.HTML
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pySCENIC
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.Python
373
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scenicplus
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
156
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cisTopic
cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics dataR
130
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SCENICprotocol
A scalable SCENIC workflow for single-cell gene regulatory network analysisPython
127
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AUCell
AUCell: score single cells with gene regulatory networksR
92
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SCope
Fast visualization tool for large-scale and high dimensional single-cell dataPython
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pycisTopic
pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.Jupyter Notebook
48
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arboreto
A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.Jupyter Notebook
45
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SCopeLoomR
R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...R
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create_cisTarget_databases
Create cisTarget databasesPython
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RcisTarget
RcisTarget: Transcription factor binding motif enrichmentHTML
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GENIE3
GENIE3 (GEne Network Inference with Ensemble of trees) R-packageC
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ScoMAP
ScoMAP is an R package to spatially integrate single-cell omics data into virtual cells and infer enhancer-to-gene relationships.R
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PUMATAC
Pipeline for Universal Mapping of ATAC-seq
Nextflow
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popscle_helper_tools
Helper tools for popscleShell
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single_cell_toolkit
Tools for correcting single cell barcodes for various scATAC-seq techniques.Shell
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GRNBoost
Scalable inference of gene regulatory networks using Apache Spark and XGBoostScala
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nextcloud_share_url_downloader
Download files from and list content of NextCloud (password protected) share directly from the command line without needing a webbrowser.Shell
16
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install_aspera_connect
Install latest version of Aspera Connect and show example how to use it for downloading sequening data.Shell
15
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pycistarget
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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scATAC-seq_benchmark
Jupyter Notebook
11
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scenicplus_analyses
SCENIC+ analysesJupyter Notebook
7
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singlecellRNA_melanoma_paper
R
7
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DeepMEL
Jupyter Notebook
6
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scenic-nf
DEPRECATED | pySCENIC pipeline implemented in Nextflow using containers
Nextflow
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Bravo_et_al_EyeAntennalDisc
Code for reproducing the figures presented in the manuscript 'Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics' (Bravo et al., 2020)HTML
5
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LoomXpy
Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulonsPython
5
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MendelCraft
The MendelCraft mod, introducing Mendelian genetics to the chickens of Minecraft!Java
5
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iterative_peak_filtering
Iterative peak filtering.Shell
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PUMATAC_tutorial
Jupyter Notebook
4
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iRegulon
A regulon consists of a transcription factor (TF) and its direct transcriptional targets, which contain common TF binding sites in their cis-regulatory control elements. The iRegulon plugin allows you to identify regulons using motif and track discovery in an existing network or in a set of co-regulated genes.Java
4
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ctxcore
Core functions for pycisTarget and the SCENIC tool suitePython
3
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scforest
scforest: a visual overview of single cell technologyTeX
3
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primescore
Calculation of regulatory impact score of a mutation.Python
3
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Bravo_et_al_Liver
Bravo_et_al_LiverJupyter Notebook
3
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hydrop_data_analysis
Jupyter Notebook
2
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webhdf5
HDF5 library in WASMPython
2
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mucistarget
Predict cis-regulatory mutations in gene regulatory networksPython
2
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ATAC-seq-analysis
Some scripts for ATAC-seq data analysisPython
2
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SCopeLoomPy
A Python notebook to create .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, compatible with SCopePython
2
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scatac_fragment_tools
Tools for working with scATAC-seq fragment filesPython
2
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AS_variant_pipeline
Allele specific variant pipelineJupyter Notebook
1
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regulatory_regions_delineation
Create regulatory regions delineationPython
1
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DGRP2_dm3_to_dm6
Create BCF/VCF files with all DGRP2 mutations for Drosophila melanogaster (dm6) from dm3 VCF files.
1
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Melanoma_MPRA_paper
Melanoma MPRA paperJupyter Notebook
1
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SpatialNF
Spatial transcriptomics NextFlow pipelinesPython
1
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EnhancerAI
Python
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