The dREG gateway is web service built on the Apache Airavata software framework and the XSEDE platform using the following software packages:
[1] dREG package: https://github.com/Danko-Lab/dREG.
The dREG package is developed to detect the divergently oriented RNA polymerase in GRO-seq, PRO-seq, or ChRO-seq data using support vector machines (e1070 or Rgtsvm package).
[2] dREG.HD package: https://github.com/Danko-Lab/dREG.HD.
The dREG.HD pa/ckage refines the location of TREs obtained using dREG by imputing DNAse-I hypersensitivity.
[3] dTOX package: https://github.com/Danko-Lab/dTOX.
The dTOX package detects transcription factor binding in PRO-seq, DNase-I-seq, and ATAC-seq using support vector machines and random forests.
[4] tfTarget package: https://github.com/Danko-Lab/tfTarget.
The tfTarget package identifies transcription factor-enhancer/promoter-gene network from run-on sequencing data
[5] BayesPrism package: https://github.com/Danko-Lab/TED.
The BayesPrism(old name:TED) package is a fully Bayesian approach to deconvolve tumor microenvironment.
[6] Rgtsvm package: https://github.com/Danko-Lab/Rgtsvm.
Rgtsvm implements support vector classification and support vector regression on a GPU to accelerate the computational speed of training and predicting large-scale models.
[7] rtfbsdb package: https://github.com/Danko-Lab/rtfbs_db.
Rtfbsdb implements TFBS scaning acorss whole genome and TF enrichment test with the aid of CIS-BP, Jolma and other TF databases.
[8] Proseq 2.0: https://github.com/Danko-Lab/proseq2.0.
Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing.
[9] Airavata PHP Gateway: https://github.com/apache/airavata-php-gateway.git.
Airavata PHP Gateway provides an API to build web sites which interact with high performance computers that are part of XSEDE.
