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mucistarget

Predict cis-regulatory mutations in gene regulatory networks

nanowgs

Nextflow pipeline for Nanopore WGS analysis

nextcloud_share_url_downloader

Download files from and list content of NextCloud (password protected) share directly from the command line without needing a webbrowser.

ngscheckmate

Software program for checking sample matching for NGS data

ngsutils

Tools for next-generation sequencing analysis

orderstatistics

OrderStatistics: Generate global ranking from distinct prioritizations from multiple heterogeneous data sources.

popscle_helper_tools

Helper tools for popscle

primescore

Calculation of regulatory impact score of a mutation.

pumatac

Pipeline for Universal Mapping of ATAC-seq

pumatac_tutorial

pycistarget

pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.

pycistopic

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

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.

rcistarget

RcisTarget: Transcription factor binding motif enrichment

rcistarget.hg19.motifdatabases

rcistarget.hg19.motifdbs.cisbponly.500bp

Database for RcisTarget

rcistarget.mm9.motifdatabases

regulatory_regions_delineation

Create regulatory regions delineation

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scatac-seq_benchmark

scenic

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

scenic-nf

DEPRECATED | pySCENIC pipeline implemented in Nextflow using containers

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.

scenicplus_analyses

SCENIC+ analyses

scenicprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis

scforest

scforest: a visual overview of single cell technology

scomap

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

scope

Fast visualization tool for large-scale and high dimensional single-cell data

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