Topic: transcription-factors Goto Github
Some thing interesting about transcription-factors
Some thing interesting about transcription-factors
transcription-factors,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.
Organization: aertslab
Home Page: http://scenic.aertslab.org
transcription-factors,pyJASPAR: A Pythonic interface to JASPAR transcription factor motifs
User: asntech
Home Page: https://pyjaspar.rtfd.io
transcription-factors,Transcription Factor Analysis Toolkit
Organization: biomeufrn
transcription-factors,geneXtendeR analysis on 547 ENCODE ChIP-seq datasets for both proximal and distal transcription factor (TF) binding peaks for all cell types
User: bohdan-khomtchouk
Home Page: https://doi.org/10.1101/082347
transcription-factors,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
User: bpucker
Home Page: https://www.tu-braunschweig.de/en/ifp/pbb
transcription-factors,Dual threshold optimization for identifying convergent evidence: TF binding locations and TF perturbation responses.
Organization: brentlab
transcription-factors,A βdata lightβ TF-network mapping algorithm using only gene expression and genome sequence data.
Organization: brentlab
transcription-factors,Bioinformatics pipeline to identify differentially active transcription factors between conditions using expression and epigenetic data
Organization: daisybio
transcription-factors,Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
Organization: danko-lab
transcription-factors,Code and resources related to the olfactory regeneration project
User: diyadas
transcription-factors,Identification and structural characterization of transcription factors based on supervised machine learning
Organization: draeger-lab
transcription-factors,Deep neural networks implemented in TensorFlow & Python for predicting whether transcription factors will bind to given DNA sequences
User: drewwiens
transcription-factors,miRinGO: Prediction of GO terms indirectly targeted by human microRNAs
User: fadeel
transcription-factors,Unofficial fork of the DeepSEA deep learning genomics project
User: henneberger
transcription-factors,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.
Organization: huising-lab
transcription-factors,7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
User: ibn-salem
Home Page: https://ibn-salem.github.io/sevenC
transcription-factors,
User: isy89
Home Page: https://lbf.readthedocs.io/en/latest/
transcription-factors,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.
User: jaleesr
transcription-factors,Identification of enriched motif pairs from chromatin interaction data
User: jhammelman
Home Page: https://spatzie.mit.edu
transcription-factors,Patterns of Binding Targets
User: jletey
Home Page: https://johnletey.github.io/PoBT/
transcription-factors,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.
User: jumitti
Home Page: https://tfinder-ipmc.streamlit.app/
transcription-factors,This is a small database of 165 manually-reviewed MADS-box family transcription factors in plants.
User: jyzhu-pointless
transcription-factors,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)
Organization: krebslabrep
transcription-factors,Single-cell Transcriptome and Regulome Analysis Pipeline
User: liulab-dfci
transcription-factors,A repository with exploration into using transformers to predict DNA β transcription factor binding
User: lucidrains
transcription-factors,[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
Organization: magics-lab
transcription-factors,Source code for the Bioconductor workshop "Integrating gene expression and DNA-binding data using R/Bioconductor"
User: mahshaaban
Home Page: https://mahshaaban.github.io/IntegratingDataBioc/
transcription-factors,target: An R Package to Predict Combined Function of Transcription Factors
User: mahshaaban
Home Page: https://bioconductor.org/packages/target/
transcription-factors,Motif discovery for DNA sequences using multiobjective optimization and genetic programming.
User: mbelmadani
Home Page: https://mbelmadani.github.io/motifgp/
transcription-factors,Netbooks is a JupyterHub catalog of use cases in gene regulatory network inference using netZoo methods..
Organization: netzoo
Home Page: https://netbooks.networkmedicine.org
transcription-factors,netZooC is a network biology package implemented in C.
Organization: netzoo
Home Page: https://netzoo.github.io/
transcription-factors,netZooM is a network biology package implemented in MATLAB.
Organization: netzoo
Home Page: https://netzoo.github.io/
transcription-factors,netZooPy is a network biology package implemented in Python.
Organization: netzoo
Home Page: https://netzoo.github.io/
transcription-factors,netZooR is a network biology package implemented in R.
Organization: netzoo
Home Page: https://netzoo.github.io/
transcription-factors,Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.
Organization: nf-core
Home Page: https://nf-co.re/tfactivity
transcription-factors,Bioinformatics study on tfbs and their association with specific tissues.
User: pentalpha
transcription-factors,An ensemble method for predicting transcription factor in protein sequences
User: raghavagps
Home Page: http://webs.iiitd.edu.in/raghava/transfacpred
transcription-factors,An R package to access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer
Organization: ropensci
Home Page: https://docs.ropensci.org/cRegulome
transcription-factors,:m: Tool for motif conservation analysis
User: saketkc
Home Page: http://saket-choudhary.me/moca
transcription-factors,Codebase for the domain adaptation (cross-species TF binding prediction) project.
Organization: seqcode
transcription-factors,An integrative toolkit for detecting cell type-specific regulators
Organization: shao-lab
transcription-factors, A motif discovery tool to detect the occurrences of known motifs
Organization: shao-lab
transcription-factors,DEbPeak - Analyze and integrate multi-omics to unravel the regulation of gene expression.
User: showteeth
transcription-factors,:bug: How to use CENTIPEDE to determine if a transcription factor is bound.
User: slowkow
Home Page: https://slowkow.github.io/CENTIPEDE.tutorial
transcription-factors,Read HOMER motif analysis output in R.
User: slowkow
transcription-factors,:dart: Human transcription factor target genes from 6 databases in convenient R format.
User: slowkow
transcription-factors,Scripts for motif assessment for HOCOMOCO v10/v11.
User: vorontsovie
Home Page: http://hocomoco.autosome.ru/
transcription-factors,R package for identifying motif matches and motif enrichment in DNA sequences
User: wkopp
transcription-factors,Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility
Organization: yoseflab
transcription-factors,Bioinformatic approach to identify functional transcription factor binding motifs
User: zeyang-shen
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