gene-regulation
There are 42 repositories under gene-regulation topic.
aertslab/arboreto
A scalable python-based framework for gene regulatory network inference using tree-based ensemble regressors.
kundajelab/ChromDragoNN
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
Danko-Lab/dREG
Detecting Regulatory Elements using GRO-seq and PRO-seq
SunXQlab/scMLnet
Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks
asntech/pyjaspar
pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs
lingfeiwang/findr
Fast Inference of Networks from Directed Regulations
markziemann/mitch
An R package for multi-dimensional pathway enrichment analysis
BrentLab/NetProphet_2.0
A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.
wassermanlab/JASPAR-UCSC-tracks
Code and data used to create the JASPAR UCSC Genome Browser tracks data hub
Genome3d/genetic_regulation_in_ASD
Analysis of regulatory impacts of autism-associated SNPs on biological pathways in the fetal and adult cortex.
santiago1234/MZT-rna-stability
Crosstalk between codon optimality and 3' UTR cis-elements dictates mRNA stability
wassermanlab/JASPAR-inference-tool
Code and data used by the JASPAR profile inference tool
calebclayreagor/DELAY
Depicting pseudotime-lagged causality for accurate gene-regulatory inference
omics-datascience/BioAPI
A powerful abstraction of gene databases
MahShaaban/target
target: An R Package to Predict Combined Function of Transcription Factors
markziemann/ART_methylation
Meta-analysis of DNA methylation in ART
r3fang/CRESTseq
CREST-seq peak calling.
zhangjunpeng411/Scan
Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data
shao-lab/MAmotif
An integrative toolkit for detecting cell type-specific regulators
TeamRegio/EpiRegioDB
Analysis and retrieval of Regulatory EleMents (REMs) linked to genes
aanderson54/Loupe_BrainTF
All code generated for Loupe et al. 2023
amirmasoudabdol/flyOpt
The Drosophila melanogaster gap genes circuit simulator, coupled with Scatter Search optimization algorithm
Genome3d/ADH_and_ALDH_regulatory_networks
Association analysis of ADH and ALDH gene regulatory interactions with GWAS traits.
jawa23bio/ChIP-Seq
ChIP-seq analysis pipeline encompassing data processing, quality control, alignment, peak calling, annotation and motif analysis.
markziemann/cistro_gmt
enabling pathway analysis of curated chip-seq data
prashnts/miriam-explore
Source code for miRiam web server and visualisation
zhangjunpeng411/SCOM
Inferring ncRNA synergistic competition
aanderson54/MAPT_cre
All code generated from Rogers et al. 2024
Genome3d/genetic_regulation_in_COPD
De novo discovery of traits co-occurring with chronic obstructive pulmonary disease.
gm1613/FLC_transcription_coupled_repression_model
Code for simulations and analysis used in Menon et al., 2024, "Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing "
GREEKC/GRAO
Gene Regulation Application Ontology
jkmckenna/smfplot
Python visualization of single locus SMF data
rujinlong/deepsmirud
Predict small molecule-mediated regulatory effects on miRNA expression
SlavovLab/nPOP
Code for the research article "Exploring functional protein covariation across single cells using nPOP". It is distributed under MIT license.