aertslab Goto Github PK

arboreto

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

as_variant_pipeline

Allele specific variant pipeline

atac-seq-analysis

Some scripts for ATAC-seq data analysis

aucell

AUCell: score single cells with gene regulatory networks

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

biopython

Official git repository for Biopython (converted from CVS)

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)

bravo_et_al_liver

Bravo_et_al_Liver

cistopic

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

create_cistarget_databases

Create cisTarget databases

ctxcore

Core functions for pycisTarget and the SCENIC tool suite

deepbrain

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

deepmel

dgrp2_dm3_to_dm6

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

fly_brain

Decoding gene regulation in the fly brain

flybrain_website

genie3

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

grnboost

Scalable inference of gene regulatory networks using Apache Spark and XGBoost

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

htslib

C library for high-throughput sequencing data formats

hydrop_data_analysis

inclusive

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

install_aspera_connect

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

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.

loompy

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

loomxpy

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

macs

MACS -- Model-based Analysis of ChIP-Seq

melanoma_mpra_paper

Melanoma MPRA paper