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1

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
425
star
2

SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
HTML
406
star
3

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
179
star
4

SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis
Python
139
star
5

cisTopic

cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data
HTML
135
star
6

AUCell

AUCell: score single cells with gene regulatory networks
R
116
star
7

SCope

Fast visualization tool for large-scale and high dimensional single-cell data
Python
69
star
8

pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
Jupyter Notebook
56
star
9

arboreto

A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
Jupyter Notebook
50
star
10

create_cisTarget_databases

Create cisTarget databases
Python
39
star
11

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
38
star
12

RcisTarget

RcisTarget: Transcription factor binding motif enrichment
HTML
31
star
13

GENIE3

GENIE3 (GEne Network Inference with Ensemble of trees) R-package
C
26
star
14

CREsted

Python
26
star
15

ScoMAP

ScoMAP is an R package to spatially integrate single-cell omics data into virtual cells and infer enhancer-to-gene relationships.
R
25
star
16

single_cell_toolkit

Tools for correcting single cell barcodes for various scATAC-seq techniques.
Shell
25
star
17

PUMATAC

Pipeline for Universal Mapping of ATAC-seq
Nextflow
21
star
18

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
21
star
19

popscle_helper_tools

Helper tools for popscle
Shell
19
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20

GRNBoost

Scalable inference of gene regulatory networks using Apache Spark and XGBoost
Scala
17
star
21

install_aspera_connect

Install latest version of Aspera Connect and show example how to use it for downloading sequening data.
Shell
16
star
22

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
13
star
23

scATAC-seq_benchmark

Jupyter Notebook
13
star
24

scenicplus_analyses

SCENIC+ analyses
Jupyter Notebook
7
star
25

singlecellRNA_melanoma_paper

R
7
star
26

LoomXpy

Python package (compatible with SCope) to create .loom files and extend them with other data e.g.: SCENIC regulons
Python
6
star
27

Nova-ST

A repository containing the analysis scripts for Nova-ST data
Jupyter Notebook
6
star
28

DeepMEL

Jupyter Notebook
6
star
29

scenic-nf

DEPRECATED | pySCENIC pipeline implemented in Nextflow using containers
Nextflow
6
star
30

DeepBrain

DeepBrain: a collection of vertebrate sequence-based enhancer models aimed at understanding brain cell type enhancer code across and within species
Jupyter Notebook
5
star
31

PUMATAC_tutorial

Jupyter Notebook
5
star
32

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
star
33

MendelCraft

The MendelCraft mod, introducing Mendelian genetics to the chickens of Minecraft!
Java
5
star
34

scatac_fragment_tools

Tools for working with scATAC-seq fragment files
Python
5
star
35

Bravo_et_al_Liver

Bravo_et_al_Liver
Jupyter Notebook
5
star
36

iterative_peak_filtering

Iterative peak filtering.
Shell
4
star
37

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
star
38

ctxcore

Core functions for pycisTarget and the SCENIC tool suite
Python
3
star
39

primescore

Calculation of regulatory impact score of a mutation.
Python
3
star
40

hydrop_data_analysis

Jupyter Notebook
3
star
41

scforest

scforest: a visual overview of single cell technology
TeX
3
star
42

webhdf5

HDF5 library in WASM
Python
2
star
43

ATAC-seq-analysis

Some scripts for ATAC-seq data analysis
Python
2
star
44

mucistarget

Predict cis-regulatory mutations in gene regulatory networks
Python
2
star
45

SpatialNF

Spatial transcriptomics NextFlow pipelines
Python
2
star
46

fly_brain

Decoding gene regulation in the fly brain
R
2
star
47

SCopeLoomPy

A Python notebook to create .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, compatible with SCope
Python
2
star
48

AS_variant_pipeline

Allele specific variant pipeline
Jupyter Notebook
1
star
49

regulatory_regions_delineation

Create regulatory regions delineation
Python
1
star
50

DGRP2_dm3_to_dm6

Create BCF/VCF files with all DGRP2 mutations for Drosophila melanogaster (dm6) from dm3 VCF files.
1
star
51

Melanoma_MPRA_paper

Melanoma MPRA paper
Jupyter Notebook
1
star
52

EnhancerAI

Python
1
star