Scripts for reproducing the poster: Co-regulation of RKIP and autophagy genes by VEZF1 and ERCC6 in prostate cancer
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Updated
Jan 19, 2019 - R
Scripts for reproducing the poster: Co-regulation of RKIP and autophagy genes by VEZF1 and ERCC6 in prostate cancer
A research compendium: Transcriptional regulation of autophagy during adipocyte differentiation
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.
Ligand-Receptor Interaction map based on scRNA-seq and pathway enrichment
Master's project - identification of trans-eQTL clusters resulting from changes in transcription factor binding site preference.
ATAC-Seq Transcription Factor Footprint Discovery and Analysis
Code for the BMC Genomics paper (Integrating binding and expression data to predict transcription factors combined function)
Build the database file for cRegulome package
Shiny app for screening for core promoter occurrences close to expressed transposons TSSs.
Build SQLite tables of microRNAs and Transcription Factors-gene Correlations
After getting the bed file from the Peak calling, we can annotate and create all downstream analysis of two sets of data
Research compendium for the preprint "Hierarchical Regulation of Autophagy During Adipocyte Differentiation"
Code for the PeerJ paper (cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer)
An R package to identify plant transcription factors from protein sequence data and classify them in families
Code for the Cells paper (Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis)
This repository enables the reproducible analysis of an important developmental neuroscience dataset on hypothalamus neuron differentiation. It performs quality control, clustering, trajectory analysis, and identification of marker genes to characterize the differentiation trajectories of glutamatergic and GABAergic Onecut3+ neuronal subtypes.
geneXtendeR analysis on 547 ENCODE ChIP-seq datasets for both proximal and distal transcription factor (TF) binding peaks for all cell types
miRinGO: Prediction of GO terms indirectly targeted by human microRNAs
An R package to access, manage and visualize regulome (microRNA/transcription factors)-gene correlations in cancer
CMTCN: A web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks
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