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Title: Regtools software      
aggregation:
composite digital object
privacy:
not applicable
refinement:
uncurated
ID:
https://doi.org/10.5281/zenodo.2575827
storedIn:
Multiple: GitHub (https://github.com/griffithlab/regtools), Zenodo (https://zenodo.org/record/2575827)
dateModified:
02-22-2019
availability:
Available
creators:
Malachi Griffith
keywords:
Software, Bioinformatics, Tool, Gene Regulation, Splicing
dateReleased:
02-22-2019
description:
Source code for the regtools application
types:
Source Code
authors:
Yang-Yang Feng, Avinash Ramu, Kelsy C Cotto, Zachary L Skidmore, Jason Kunisaki, Donald F Conrad, Yiing Lin, William Chapman, Ravindra Uppaulri, Ramaswamy Govindan, Obi L Griffith, Malachi Griffith
publicationVenue:
bioRXiv (Cold Spring Harbor Laboratory Press)
description:
The interpretation of variants in cancer is frequently focused on direct protein coding alterations. However, this analysis strategy excludes somatic mutations in non-coding regions of the genome and even exonic mutations may have unidentified non-coding consequences. Here we present RegTools, a software package designed to integrate analysis of somatic variant calls from genomic data with splice junctions extracted from transcriptomic data in order to efficiently identify variants that may cause aberrant splicing in tumors. RegTools is open source (MIT license) and freely available as source code or as a Docker image (http://regtools.org/).
ID:
https://doi.org/10.1101/436634
acknowledges:
NIH
title:
RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer
dateReleased:
11-25-2018
name:
N/A
name:
N/A
identifier:
HG007940
funders:
NIH (NHGRI)
description:
This work was supported by a grant to Malachi Griffith from the National Human Genome Research Institute (NHGRI) of the NIH under award number R00HG007940. Creation of these data objects was supported by the NIH BD2K Cloud Credits Commons Pilot Program (CCREQ-2017-03-00071).
count:
1
primary:
True
title:
Regtools software
storedIn:
https://github.com/
description:
Release of regtools open source software
size:
19
unit:
MB
ID:
SCR:016270
name:
CEDAR Workbench
abbreviation:
CEDAR
homePage: https://cedar.metadatacenter.org