transcription-factor-binding-site
There are 15 repositories under transcription-factor-binding-site topic.
MAGICS-LAB/DNABERT_2
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
benoukraflab/TFregulomeR-old
TFregulomeR reveals transcription factors’ context-specific features and functions
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.
benoukraflab/TFregulomeR
TFregulomeR reveals transcription factors’ context-specific features and functions
kchu25/MOTIFs.jl
DNA Motif discovery that includes the discovery of flexible (long or gapped) motifs.
ANSES-Ploufragan/SIGffRid
Find two-boxes transcription factor binding sites (made for sigma factor binding sites) by comparing intergenic DNA regions upstream pairs of orthologous genes using statistical analyses
linquynus/TFregulomeR-dev
TFregulomeR reveals transcription factors’ context-specific features and functions
bioinfodlsu/rice-pilaf
Published in GigaScience. Web app for post-GWAS/QTL analysis that performs a slew of novel bioinformatics analyses to cross-reference GWAS/QTL mapping results with a host of publicly available rice databases
chaolinzhanglab/PlotPWM.jl
Plot position weight matrices (PWM)
kchu25/UnfoldCDL.jl
Deep Unfolded Convolutional Dictionary Learning for motif discovery.
Secret-Ambush/Identifying-Anchor-Residues-in-TFBS
Anchor Residue Identification for any TF
dogmaticcentral/progesterone
Which ESR1 and PGR binding sites are functional?
uds-helms/MutaNET
Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.
lchmo444/TFBSinG
Prediction of the binding sites of multiple transcription factors in a whole genome