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General utilities/ convenience scripts useful for munging genomic data.
A data-driven method to identify allele-specific differences in distributed functional genomic marks
Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data
The R package for SVM with GPU architecture based on the GTSVM software
Refining TRE regions from dREG by imputing DHS.
Mirror of Apache Airavata PHP Gateway
Tutorials covering various topics in genomic data analysis.
Detecting Regulatory Elements using GRO-seq and PRO-seq
Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
Danko lab website
Analyses for an initial paper on the evolutionary CD4+ T-cell PRO-seq datasets.
Tus server in Laravel PHP 4.2
Analyze mechanisms of tamoxifen resistence in MCF-7 subclones
4DN web site
Inference of transcript stability from polyA and 5' splice site sequence elements
Calculate a sort of 'information content' for data in bed format, by seeing how many unique positions are recovered as a function of the total read depth.
Identifies Pol II 'waves' in GRO-seq or PRO-seq with support for bigWig files.
Models used for running dREG