jkmckenna/smfplot

Python visualization of single locus SMF data

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markziemann/mitch

An R package for multi-dimensional pathway enrichment analysis

Language: R - Size: 9.44 MB - Last synced: 2 days ago - Pushed: about 1 month ago - Stars: 15 - Forks: 4

omics-datascience/BioAPI

A powerful abstraction of gene databases

Language: Python - Size: 13.1 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 5 - Forks: 0

jawa23bio/ChIP-Seq

ChIP-seq analysis pipeline encompassing data processing, quality control, alignment, peak calling, annotation and motif analysis.

Size: 1.49 MB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 1 - Forks: 0

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 "

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markziemann/ART_methylation

Meta-analysis of DNA methylation in ART

Language: R - Size: 196 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 3 - Forks: 2

markziemann/cistro_gmt

enabling pathway analysis of curated chip-seq data

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markziemann/dee2_gene_signatures

A resource of gene expression signatures derived from the DEE2 dataset (http://dee2.io)

Language: R - Size: 94.7 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

markziemann/mitch_legacy

An R package for multi-dimensional pathway enrichment analysis (legacy repo)

Language: R - Size: 78.5 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

markziemann/scsimde

simulating dysregulated gene expression in single cell transcriptome data

Language: R - Size: 16.6 KB - Last synced: about 1 month ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

asntech/pyjaspar

pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs

Language: Python - Size: 53.8 MB - Last synced: 23 days ago - Pushed: 3 months ago - Stars: 18 - Forks: 1

zhangjunpeng411/Scan

Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data

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aanderson54/Loupe_BrainTF

All code generated for Loupe et al. 2023

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aertslab/arboreto

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

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wassermanlab/JASPAR-inference-tool

Code and data used by the JASPAR profile inference tool

Language: Python - Size: 390 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 6 - Forks: 1

wassermanlab/JASPAR-UCSC-tracks

Code and data used to create the JASPAR UCSC Genome Browser tracks data hub

Language: Python - Size: 304 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 11 - Forks: 5

th789/fflmediation

R package to predict gene feed forward loops using mediation analysis. Analyses integrate observed miRNA and mRNA expression data and database information on gene interactions.

Language: R - Size: 71.7 MB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

SunXQlab/scMLnet

Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks

Language: R - Size: 12.9 MB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 20 - Forks: 8

Genome3d/genetic_regulation_in_COPD

De novo discovery of traits co-occurring with chronic obstructive pulmonary disease.

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Genome3d/ADH_and_ALDH_regulatory_networks

Association analysis of ADH and ALDH gene regulatory interactions with GWAS traits.

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lingfeiwang/findr

Fast Inference of Networks from Directed Regulations

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aanderson54/MAPT_cre

All code generated from Rogers et al. 2023

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TeamRegio/EpiRegioDB

Analysis and retrieval of Regulatory EleMents (REMs) linked to genes

Language: Python - Size: 60.6 MB - Last synced: 8 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 2

ZJUFanLab/SpaTrio

Language: Python - Size: 74.5 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 4 - Forks: 1

calebclayreagor/DELAY

Depicting pseudotime-lagged causality for accurate gene-regulatory inference

Language: Python - Size: 359 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 0

kundajelab/ChromDragoNN

Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"

Language: Jupyter Notebook - Size: 1.27 MB - Last synced: 8 months ago - Pushed: about 3 years ago - Stars: 40 - Forks: 11

zhangjunpeng411/SCOM

Inferring ncRNA synergistic competition

Language: R - Size: 20.2 MB - Last synced: 21 days ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

Genome3d/genetic_regulation_in_ASD

Analysis of regulatory impacts of autism-associated SNPs on biological pathways in the fetal and adult cortex.

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rujinlong/deepsmirud Fork of 2003100127/deepsmirud

Predict small molecule-mediated regulatory effects on miRNA expression

Language: Python - Size: 1.18 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

BCMSLab/hierarchical_autophagy_regulation

Research compendium for the preprint "Hierarchical Regulation of Autophagy During Adipocyte Differentiation"

Language: R - Size: 40 KB - Last synced: 10 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

Danko-Lab/dREG

Detecting Regulatory Elements using GRO-seq and PRO-seq

Language: R - Size: 221 MB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 30 - Forks: 20

omarcodex/geneOS

Gene regulation exploring with OOP

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prashnts/miriam-explore 📦

Source code for miRiam web server and visualisation

Language: HTML - Size: 211 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 1

MahShaaban/target

target: An R Package to Predict Combined Function of Transcription Factors

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BrentLab/NetProphet_2.0

A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.

Language: R - Size: 86.8 MB - Last synced: 8 months ago - Pushed: about 3 years ago - Stars: 12 - Forks: 5

santiago1234/MZT-rna-stability

Crosstalk between codon optimality and 3' UTR cis-elements dictates mRNA stability

Language: Jupyter Notebook - Size: 127 MB - Last synced: over 1 year ago - Pushed: over 2 years ago - Stars: 4 - Forks: 0

GREEKC/GRAO

Gene Regulation Application Ontology

Size: 77.1 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

shao-lab/MAmotif

An integrative toolkit for detecting cell type-specific regulators

Language: Python - Size: 15.7 MB - Last synced: 22 days ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0

r3fang/CRESTseq

CREST-seq peak calling.

Language: C++ - Size: 2.21 MB - Last synced: over 1 year ago - Pushed: almost 7 years ago - Stars: 3 - Forks: 0

Genome3d/blood-metabolites-regulation

Language: Python - Size: 14.2 MB - Last synced: over 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

amirmasoudabdol/flyOpt

The Drosophila melanogaster gap genes circuit simulator, coupled with Scatter Search optimization algorithm

Language: C - Size: 524 KB - Last synced: about 1 month ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0