Explore @aertslab Open Source projects

@aertslab

aertslab

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Registered about 11 years ago
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Python
31.3 %

Jupyter Notebook
25.0 %

R
12.5 %

Shell
10.4 %

HTML
6.3 %

Java
4.2 %

Nextflow 4.2 %

Scala
2.1 %

C
2.1 %

TeX
2.1 %
Location 🇧🇪 Belgium
Country Total Rank 88
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Nextflow 1

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SCENIC

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

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

cisTopic

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

SCENICprotocol

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

AUCell

AUCell: score single cells with gene regulatory networks

SCope

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

pycisTopic

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

Jupyter Notebook

arboreto

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

Jupyter Notebook

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, ...

create_cisTarget_databases

Create cisTarget databases

RcisTarget

RcisTarget: Transcription factor binding motif enrichment

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.

PUMATAC

Pipeline for Universal Mapping of ATAC-seq

popscle_helper_tools

Helper tools for popscle

single_cell_toolkit

Tools for correcting single cell barcodes for various scATAC-seq techniques.

GRNBoost

Scalable inference of gene regulatory networks using Apache Spark and XGBoost

nextcloud_share_url_downloader

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

install_aspera_connect

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

pycistarget

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

Jupyter Notebook

scATAC-seq_benchmark

Jupyter Notebook

scenicplus_analyses

SCENIC+ analyses

Jupyter Notebook

singlecellRNA_melanoma_paper

DeepMEL

Jupyter Notebook

scenic-nf

DEPRECATED | pySCENIC pipeline implemented in Nextflow using containers

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)

LoomXpy

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

MendelCraft

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

iterative_peak_filtering

Iterative peak filtering.

PUMATAC_tutorial

Jupyter Notebook

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.

ctxcore

Core functions for pycisTarget and the SCENIC tool suite

scforest

scforest: a visual overview of single cell technology

primescore

Calculation of regulatory impact score of a mutation.

Bravo_et_al_Liver

Bravo_et_al_Liver

Jupyter Notebook

hydrop_data_analysis

Jupyter Notebook

webhdf5

HDF5 library in WASM

mucistarget

Predict cis-regulatory mutations in gene regulatory networks

ATAC-seq-analysis

Some scripts for ATAC-seq data analysis

fly_brain

Decoding gene regulation in the fly brain

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

scatac_fragment_tools

Tools for working with scATAC-seq fragment files

AS_variant_pipeline

Allele specific variant pipeline

Jupyter Notebook

regulatory_regions_delineation

Create regulatory regions delineation

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

Jupyter Notebook

SpatialNF

Spatial transcriptomics NextFlow pipelines

EnhancerAI