transcription-factors

There are 1 repository under transcription-factors topic.

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.
single-cell transcriptomics gene-regulatory-network transcription-factors
Language:Python 538
MAGICS-LAB / DNABERT_2
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
dataset dna dna-processing dna-training genome genome-analysis language-model covid promoter promoter-analysis promoters splice splice-site transcription-factor-binding transcription-factor-binding-site transcription-factors
Language:Shell 417
liulab-dfci / MAESTRO
Single-cell Transcriptome and Regulome Analysis Pipeline
scatac-seq scrna-seq epigenetics snakemake-workflows transcription-factors gene-regulatory-networks
Language:C 291
netZoo / netZooR
netZooR is a network biology package implemented in R.
gene-regulatory-network transcription-factors
Language:R 106
slowkow / tftargets
:dart: Human transcription factor target genes from 6 databases in convenient R format.
bioinformatics data rstats transcription-factors
Language:R 86
lucidrains / tf-bind-transformer
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
artificial-intelligence deep-learning transformers attention-mechanism transcription-factor-binding transcription-factors gene-expression
Language:Python 84
netZoo / netZooPy
netZooPy is a network biology package implemented in Python.
gene-regulatory-network transcription-factors
Language:Jupyter Notebook 84
netZoo / netbooks
Netbooks is a JupyterHub catalog of use cases in gene regulatory network inference using netZoo methods..
gene-regulatory-network transcription-factors
Language:Jupyter Notebook 40
jaleesr / BITFAM
BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.
r scrna-seq-analysis transcription-factors single-cell rna-seq scrna-seq scrnaseq-data bayesian-inference
Language:R 31
netZoo / netZooM
netZooM is a network biology package implemented in MATLAB.
gene-regulatory-network transcription-factors
Language:MATLAB 27
netZoo / netZooC
netZooC is a network biology package implemented in C.
gene-regulatory-network transcription-factors
Language:C 26
slowkow / CENTIPEDE.tutorial
:bug: How to use CENTIPEDE to determine if a transcription factor is bound.
tutorial bioinformatics enrichment dnase-seq transcription-factors rstats
Language:R 26
asntech / pyjaspar
pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs
gene-regulation motif-discovery transcription-factors
Language:Python 25
Danko-Lab / rtfbs_db
Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
transcription-factors transcription-factor-binding motif tfbs-discovery enrichment-analysis cis-bp r
Language:R 23
shao-lab / MotifScan
A motif discovery tool to detect the occurrences of known motifs
bioinformatics transcription-factors motif-discovery
Language:Python 20
Jumitti / TFinder
Python script to quickly extract promoter and terminator regions with the NCBI API. Search for the presence of individual pattern or transcription factor responsive elements with manual sequence (IUPAC) or JASPAR API.
api dna dna-sequences iupac jaspar ncbi promoter-sequences python python3 responsive-elements streamlit terminator-sequences transcription-factor transcription-factor-binding-site transcription-factors webtools
Language:Python 16
slowkow / homerkit
Read HOMER motif analysis output in R.
bioinformatics transcription-factors enrichment rstats
Language:R 16
drewwiens / TensorFlow-DNNs-for-Predicting-DNA-Transcription-Factor-Binding
Deep neural networks implemented in TensorFlow & Python for predicting whether transcription factors will bind to given DNA sequences
deep-neural-networks transcription-factors tensorflow dna-sequences machine-learning bioinformatics
Language:Python 15
daisybio / TF-Prioritizer
Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data
bioinformatics-pipeline transcription-factors
Language:Java 14
BrentLab / NetProphet_2.0
A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.
gene-expression gene-regulation transcription-factors transcriptional-regulatory-network
Language:R 13
MybMonday
bpucker / MybMonday
MYB transcription factors are one of the largest gene family in plants and control many processes. This repository provides additional background to the #MYB_Monday tweets
transcription gene-expression transcription-factors r2r3-myb myb plants genomics
Language:Python 12
ibn-salem / sevenC
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
chip-seq hi-c chromatin-interaction sequence-motif transcription-factors prediction r-package 3d-genome
Language:R 12
Isy89 / LBF
bioinformatics cfdna cli feature-extraction liquid-biopsy plugin-system python3 transcription-factor-binding-site transcription-factors tui transcription-start-site differential-transcription-factors-activity biomarker-discovery fragmentomics
Language:Python 12
seqcode / cross-species-domain-adaptation
Codebase for the domain adaptation (cross-species TF binding prediction) project.
comparative-genomics deep-learning domain-adaptation genomics transcription-factors
Language:Jupyter Notebook 12
nf-core / tfactivity
Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
nextflow nf-core open-chromatin-regions pipeline transcription-factors transcriptomics workflow
Language:Nextflow 11
YosefLab / epitome
Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility
chromatin-accessibility dnase-seq atac-seq epigenetic-events transcription-factors histone-modifications
Language:Python 10
zeyang-shen / maggie
Bioinformatic approach to identify functional transcription factor binding motifs
bioinformatics transcription-factors genetic-variants motif-analysis dna-sequences
Language:Python 10
saketkc / moca
:m: Tool for motif conservation analysis
motif-discovery bioinformatics transcription-factor-binding transcription-factors chip-seq
Language:PostScript 9
showteeth / DEbPeak
DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression.
analysis chip-seq integration rna-seq visualization atac-seq differential-expression transcription-factors count-matrix geo m6a-seq peak-related
Language:HTML 8
draeger-lab / TFpredict
Identification and structural characterization of transcription factors based on supervised machine learning
bioinformatics blast fasta homology identification machine-learning prediction sabine transcription-factor transcription-factors
Language:Java 7
mbelmadani / motifgp
Motif discovery for DNA sequences using multiobjective optimization and genetic programming.
motif genetic-programming multiobjective-optimization bioinformatics chip-seq regular-expressions network-expressions strongly-typed motif-discovery transcription-factors transcription-factor-binding python pareto-front nsga-ii deap dna sequences dna-sequences jaspar
Language:Python 6
SaniyaKhullar / NetREm
Network Regression Embeddings reveal cell-type Transcription Factor coordination for target gene (TG) regulation
bioinformatics-software gene-regulatory-network-inference multiomics-data network-lasso network-regularization ppi-networks transcription-factors transcriptional-regulatory-network regression-embeddings regularization-embeddings transcription-factor-coordination network-based-inference network-guided-regression predictor-interactions regression-with-prior-knowledge netrem single-cell-analysis gene-expression-profiles protein-interaction
Language:Jupyter Notebook 6
epiRomics
Huising-Lab / epiRomics
An R package designed to integrate and visualize various levels of epigenomic information, including but not limited to: ChIP, Histone, ATAC, and RNA sequencing. epiRomics is also designed to identify enhancer and enhanceosome regions from these data.
enhancer atac-seq r-package data-visualization chip-seq histone chromatin-accessibiity enhancer-prediction transcription-factors transcription-factor-binding regulatory-network epigenetics epigenomics multi-omics rna-seq ucsc-browser regulome-analysis
Language:HTML 5
raghavagps / transfacpred
An ensemble method for predicting transcription factor in protein sequences
alignment-free bioinformatics blast hybrid-approach machine-learning-algorithms transcription-factors
Language:Python 5
aanderson54 / Loupe_BrainTF
All code generated for Loupe et al. 2023
brain chip-seq gene-regulation psychiatric-disorders transcription-factors
Language:HTML 4
Krebslabrep / Kreibich_2023_5mC_at_enhancers
Analysis of Single Molecule Footprinting (SMF) data for the analysis of DNA methylation, chromatin accessibility and TF binding. The repository contains all primary code to reproduce the main analyses for the publication "Single molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation" (Kreibich et al., 2023)
chromatin-accessibiity dna-methylation epigenetics transcription-factors single-molecule-footprinting
Language:R 4

transcription-factors

aertslab / pySCENIC

MAGICS-LAB / DNABERT_2

liulab-dfci / MAESTRO

netZoo / netZooR

slowkow / tftargets

lucidrains / tf-bind-transformer

netZoo / netZooPy

netZoo / netbooks

jaleesr / BITFAM

netZoo / netZooM

netZoo / netZooC

slowkow / CENTIPEDE.tutorial

asntech / pyjaspar

Danko-Lab / rtfbs_db

shao-lab / MotifScan

Jumitti / TFinder

slowkow / homerkit

drewwiens / TensorFlow-DNNs-for-Predicting-DNA-Transcription-Factor-Binding

daisybio / TF-Prioritizer

BrentLab / NetProphet_2.0

bpucker / MybMonday

ibn-salem / sevenC

Isy89 / LBF

seqcode / cross-species-domain-adaptation

nf-core / tfactivity

YosefLab / epitome

zeyang-shen / maggie

saketkc / moca

showteeth / DEbPeak

draeger-lab / TFpredict

mbelmadani / motifgp

SaniyaKhullar / NetREm

Huising-Lab / epiRomics

raghavagps / transfacpred

aanderson54 / Loupe_BrainTF

Krebslabrep / Kreibich_2023_5mC_at_enhancers