aertslab/pycisTopic

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

Language: Jupyter Notebook - Size: 33.5 MB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 74 - Forks: 12

aertslab/TF-MInDi

Transcription Factor Motifs and Instances Discovery

Language: Python - Size: 10.1 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 6 - Forks: 0

aertslab/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.

Language: Python - Size: 34.8 MB - Last synced at: 12 days ago - Pushed at: 2 months ago - Stars: 533 - Forks: 195

aertslab/CREsted-paper

Language: Jupyter Notebook - Size: 134 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 2 - Forks: 0

aertslab/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, ...

Language: R - Size: 1.6 MB - Last synced at: 11 days ago - Pushed at: over 3 years ago - Stars: 43 - Forks: 15

aertslab/CREsted

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

Language: Python - Size: 95 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 44 - Forks: 8

aertslab/GRNBoost 📦

Scalable inference of gene regulatory networks using Apache Spark and XGBoost

Language: Scala - Size: 3.87 MB - Last synced at: about 1 month ago - Pushed at: over 7 years ago - Stars: 21 - Forks: 2

aertslab/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.

Language: Jupyter Notebook - Size: 40.9 MB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 228 - Forks: 43

aertslab/create_cisTarget_databases

Create cisTarget databases

Language: Python - Size: 526 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 52 - Forks: 7

aertslab/SCENIC

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

Language: HTML - Size: 267 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 451 - Forks: 97

aertslab/ctxcore

Core functions for pycisTarget and the SCENIC tool suite

Language: Python - Size: 6.06 MB - Last synced at: 17 days ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 7

aertslab/cisTopic

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

Language: HTML - Size: 187 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 140 - Forks: 28

aertslab/Nova-ST

A repository containing the analysis scripts for Nova-ST data

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aertslab/SpatialNF

Spatial transcriptomics NextFlow pipelines

Language: Python - Size: 41.9 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

aertslab/pycistarget

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

Language: Python - Size: 5.74 MB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 17 - Forks: 4

aertslab/SCope

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

Language: Python - Size: 32.9 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 69 - Forks: 15

aertslab/DeepBrain

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

Language: Jupyter Notebook - Size: 2.42 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 6 - Forks: 0

aertslab/install_aspera_connect

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

Language: Shell - Size: 3.91 KB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 19 - Forks: 9

aertslab/single_cell_toolkit

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

Language: Shell - Size: 347 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 26 - Forks: 3

aertslab/scatac_fragment_tools

Tools for working with scATAC-seq fragment files

Language: Python - Size: 101 KB - Last synced at: 3 months ago - Pushed at: 6 months ago - Stars: 6 - Forks: 0

aertslab/regulatory_regions_delineation

Create regulatory regions delineation

Language: Python - Size: 81.1 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

aertslab/PUMATAC

Pipeline for Universal Mapping of ATAC-seq

Language: Nextflow - Size: 651 KB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 24 - Forks: 1

aertslab/PUMATAC_tutorial

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aertslab/scATAC-seq_benchmark

Language: Jupyter Notebook - Size: 633 MB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 15 - Forks: 2

aertslab/hydrop_data_analysis

Language: Jupyter Notebook - Size: 255 MB - Last synced at: 10 months ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 3

aertslab/LoomXpy

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

Language: Python - Size: 169 KB - Last synced at: 17 days ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 2

aertslab/scforest

scforest: a visual overview of single cell technology

Language: TeX - Size: 16 MB - Last synced at: 10 months ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 0

aertslab/nextcloud_share_url_downloader

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

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aertslab/arboreto

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

Language: Jupyter Notebook - Size: 63.9 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 47 - Forks: 24

aertslab/AUCell

AUCell: score single cells with gene regulatory networks

Language: R - Size: 10.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 92 - Forks: 26

aertslab/RcisTarget

RcisTarget: Transcription factor binding motif enrichment

Language: HTML - Size: 82.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 28 - Forks: 8

aertslab/shap Fork of shap/shap

A game theoretic approach to explain the output of any machine learning model.

Language: Jupyter Notebook - Size: 260 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

aertslab/ScoMAP

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

Language: R - Size: 3.79 MB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 20 - Forks: 4

aertslab/GENIE3

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

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aertslab/DeepMEL

Language: Jupyter Notebook - Size: 219 KB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 5

aertslab/SCENICprotocol

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

Language: Python - Size: 211 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 116 - Forks: 61

aertslab/scenicplus_analyses

SCENIC+ analyses

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aertslab/spatial_fly_website

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aertslab/scanpy Fork of scverse/scanpy

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

Size: 24.4 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

aertslab/NGSCheckMate Fork of parklab/NGSCheckMate

Software program for checking sample matching for NGS data

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aertslab/RcisTarget.mm9.motifDatabases

Size: 0 Bytes - Last synced at: about 2 years ago - Pushed at: about 9 years ago - Stars: 0 - Forks: 0

aertslab/ToucanJS

Language: JavaScript - Size: 2.99 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

aertslab/samtools Fork of samtools/samtools

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

Language: C - Size: 11.2 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

aertslab/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

Language: Python - Size: 6.84 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

aertslab/singlecellRNA_melanoma_paper

Language: R - Size: 111 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 8

aertslab/ngsutils Fork of ngsutils/ngsutils

Tools for next-generation sequencing analysis

Language: Python - Size: 5.4 MB - Last synced at: about 2 years ago - Pushed at: over 10 years ago - Stars: 0 - Forks: 0

aertslab/primescore

Calculation of regulatory impact score of a mutation.

Language: Python - Size: 3.4 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 2

aertslab/RcisTarget.hg19.motifDatabases

Size: 0 Bytes - Last synced at: about 2 years ago - Pushed at: about 9 years ago - Stars: 0 - Forks: 0

aertslab/mucistarget

Predict cis-regulatory mutations in gene regulatory networks

Language: Python - Size: 127 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 0

aertslab/nanowgs Fork of jdemeul/nanowgs

Nextflow pipeline for Nanopore WGS analysis

Size: 162 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

aertslab/orderstatistics

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

Language: Java - Size: 3.05 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

aertslab/MACS Fork of macs3-project/MACS

MACS -- Model-based Analysis of ChIP-Seq

Language: Python - Size: 163 MB - Last synced at: about 2 years ago - Pushed at: over 10 years ago - Stars: 0 - Forks: 1

aertslab/grpc-bus Fork of gabrielgrant/grpc-bus

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

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aertslab/loompy Fork of linnarsson-lab/loompy

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

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aertslab/Melanoma_MPRA_paper

Melanoma MPRA paper

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aertslab/grpc-bus-websocket-proxy-client Fork of gabrielgrant/grpc-bus-websocket-proxy-client

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

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aertslab/INCLUSive

motif finding library and application that can be used to search for potential transcription factors.

Language: C++ - Size: 542 KB - Last synced at: about 2 years ago - Pushed at: about 9 years ago - Stars: 0 - Forks: 0

aertslab/iterative_peak_filtering

Iterative peak filtering.

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aertslab/FlyBrain_website

Language: R - Size: 74.3 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

aertslab/bcftools Fork of samtools/bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

Language: C - Size: 5.44 MB - Last synced at: about 2 years ago - Pushed at: over 10 years ago - Stars: 0 - Forks: 0

aertslab/AS_variant_pipeline

Allele specific variant pipeline

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aertslab/ATAC-seq-analysis

Some scripts for ATAC-seq data analysis

Language: Python - Size: 11.7 KB - Last synced at: about 2 years ago - Pushed at: over 9 years ago - Stars: 2 - Forks: 3

aertslab/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)

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aertslab/popscle_helper_tools

Helper tools for popscle

Language: Shell - Size: 38.1 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 15 - Forks: 6

aertslab/MendelCraft

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

Language: Java - Size: 1.37 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 1

aertslab/Bravo_et_al_Liver

Bravo_et_al_Liver

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aertslab/scenic-nf 📦

DEPRECATED | pySCENIC pipeline implemented in Nextflow using containers

Language: Nextflow - Size: 45.2 MB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 4

aertslab/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.

Language: Java - Size: 591 MB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 1

aertslab/fly_brain

Decoding gene regulation in the fly brain

Language: R - Size: 22 MB - Last synced at: 11 days ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 0

aertslab/scatac_benchmark

Language: Jupyter Notebook - Size: 624 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

aertslab/DGRP2_dm3_to_dm6

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

Size: 10.7 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

aertslab/webhdf5

HDF5 library in WASM

Language: Python - Size: 5.86 KB - Last synced at: 22 days ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 2

aertslab/RcisTarget.hg19.motifDBs.cisbpOnly.500bp

Database for RcisTarget

Size: 213 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

aertslab/biopython Fork of biopython/biopython

Official git repository for Biopython (converted from CVS)

Language: Python - Size: 69.1 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

aertslab/htslib Fork of samtools/htslib

C library for high-throughput sequencing data formats

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aertslab/toucan

TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes : comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes. It is a platform independent, standalone Java application that is tightly linked with Ensembl, and was built using the BioJava package. SOAP web services are used to remotely access multiple algorithms for comparative genomics, motif detection, and module detection.

Language: Java - Size: 11.4 MB - Last synced at: almost 2 years ago - Pushed at: almost 11 years ago - Stars: 0 - Forks: 0