aertslab

SCENICprotocol

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

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, ...

GENIE3

GENIE3 (GEne Network Inference with Ensemble of trees) R-package

ScoMAP

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

install_aspera_connect

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

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)

singlecellRNA_melanoma_paper

DeepMEL

scenic-nf

DEPRECATED | pySCENIC pipeline implemented in Nextflow using containers

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.

iterative_peak_filtering

Iterative peak filtering.

hydrop_data_analysis

primescore

Calculation of regulatory impact score of a mutation.

scforest

scforest: a visual overview of single cell technology

fly_brain

Decoding gene regulation in the fly brain

mucistarget

Predict cis-regulatory mutations in gene regulatory networks

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

webhdf5

HDF5 library in WASM

DGRP2_dm3_to_dm6

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

Melanoma_MPRA_paper

Melanoma MPRA paper

regulatory_regions_delineation

Create regulatory regions delineation

AS_variant_pipeline

Allele specific variant pipeline

grpc-bus

Call GRPC services (even streams!) from the browser over any two-way socket to Node and soon Go.

grpc-bus-websocket-proxy-client

Connect to any GRPC service from a browser via a WebSocket Proxy Server

loompy

Python implementation of the Loom file format - http://loompy.org

nanowgs

Nextflow pipeline for Nanopore WGS analysis

NGSCheckMate

Software program for checking sample matching for NGS data

orderstatistics

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

samtools

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

scanpy

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