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transcription-factor-binding

Here are 38 public repositories matching this topic...

ubercomrade / MultiDeNA

Pipeline for integration different models of transcription factor binding sites

bioinformatics transcription-factors cython python3 transcription-factor-binding

Updated Nov 8, 2024
Python

maxATAC

MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

chip-seq deeplearning atac-seq transcription-factor-binding genome-analysis maxatac

Updated Oct 18, 2024
Python

MAGICS-LAB / DNABERT_2

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

transcription-factors genome splice dna dataset promoters promoter transcription-factor-binding language-model genome-analysis promoter-analysis transcription-factor-binding-site covid dna-processing splice-site dna-training

Updated Aug 23, 2024
Shell

crazyhottommy / ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

chip-seq histone-modifications transcription-factor-binding

Updated Aug 5, 2024
Python

jawa23bio / ChIP-Seq

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

gene-regulation transcription-factor-binding chip-seq-pipeline

Updated May 14, 2024

asntech / pyjaspar

pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs

transcription-factors gene-regulation transcription-factor-binding motif-discovery jaspar motifs tf-binding-motif

Updated Mar 23, 2024
Python

zanarashidi / transcription-factor-binding

Transcription Factor (TF) binding preference prediction using deep neural networks.

pytorch convolutional-neural-networks transcription-factor-binding dna-sequences pfm sequence-logo binding-prediction doublet-shuffle

Updated Jan 15, 2024
Python

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.

transcription-factors rna-seq data-visualization epigenetics chip-seq histone atac-seq r-package enhancer transcription-factor-binding ucsc-browser regulatory-network epigenomics multi-omics enhancer-prediction chromatin-accessibiity regulome-analysis

Updated Nov 18, 2023
HTML

dansta0804 / TF_analysis

Repozitorijoje saugomi failai, implementuojantys R Shiny aplikaciją ir leidžiantys vertinti įkeltų genominių duomenų kokybę bei vykdyti biologines analizes.

r genome-annotation chip-seq transcription-factor-binding pwm shinydashboard genomic-regions homo-sapiens peak-calling mus-musculus

Updated Jun 14, 2023
R

dohlee / bpnet-pytorch

Implementation of BPNet, a base-resolution convolutional neural network for transcription-factor binding prediction, in PyTorch.

bioinformatics deep-learning biology computational-biology transcription-factor-binding reproduction reproduction-code

Updated May 7, 2023
Python

saketkc / moca

Ⓜ️ Tool for motif conservation analysis

bioinformatics transcription-factors chip-seq transcription-factor-binding motif-discovery

Updated Jun 23, 2022
PostScript

pinellolab / haystack_bio

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Updated Jun 21, 2022
HTML

BrentLab / Dual_Threshold_Optimization

Dual threshold optimization for identifying convergent evidence: TF binding locations and TF perturbation responses.

transcription-factors transcription-factor-binding transcriptional-regulatory-network transcription-factor-perturbation

Updated Jun 17, 2022
Python

lucidrains / tf-bind-transformer

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

transcription-factors deep-learning transformers gene-expression artificial-intelligence transcription-factor-binding attention-mechanism

Updated Jun 2, 2022
Python

draeger-lab / SABINE

Prediction of the binding specificity of transcription factors using support vector regression

transcription-factor-binding sequence-prediction protein-dna-interactions bioinformatics-tool

Updated Feb 14, 2022
Java

remap-cisreg / ReMapEnrich

ReMapEnrich is a R-software package to identify significantly enriched regions from ReMap catalogues or user defined catalogues. ReMapEnrich provide functions to import any in-house catalogue, automate and plot the enrichment analysis for genomic regions.

r chip-seq r-package transcription-factor-binding enrichment-analysis genomic-regions

Updated Feb 2, 2022
HTML

ytabatabaee / TF_Binding_Prediction

Predicting transcription factor-DNA binding from sequence

motif chip-seq transcription-factor-binding dna-binding-proteins

Updated Dec 17, 2021
Jupyter Notebook

kchu25 / MotifPvalue.jl

Threshold and p-value computations for Position Weight Matrices

bioinformatics genomics julia motif p-value transcription-factor-binding pwm motifs position-weight-matrix regulatory-genomics

Updated Dec 15, 2021
Julia

mahossam / DNA-Transcription-Factor-Binding-Prediction

DNA Transcription Factor Binding Prediction (Self-learning Project)

deep-learning biology computational-biology dna transcription-factor-binding dna-sequences biological-data

Updated Aug 11, 2021
Jupyter Notebook

brlauuu / motevowrapper

Simple Python parser for MotEvo.

motif transcription-factor-binding tfbs-discovery motevo

Updated May 25, 2021
Python

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