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Keep Me Around: Intron Retention Detection and Analysis

Pimentel, Harold and Conboy, John G. and Pachter, Lior (2016) Keep Me Around: Intron Retention Detection and Analysis. . (Submitted)

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We present a tool, keepme around (kma), a suite of python scripts and an R package that finds retained introns in RNA-Seq experiments and incorporates biological replicates to reduce the number of false positives when detecting retention events. kma uses the results of existing quantification tools that probabilistically assign multi-mapping reads, thus interfacing easily with transcript quantification pipelines. The data is represented in a convenient, database style format that allows for easy aggregation across introns, genes, samples, and conditions to allow for further exploratory analysis.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper
Pachter, Lior0000-0002-9164-6231
Additional Information:Submitted on 2 Oct 2015. October 5, 2015 HP was supported by the NSF GRFP. JGC and LP were supported in part by NIH R01 DK094699.
Funding AgencyGrant Number
NSF Graduate Research FellowshipUNSPECIFIED
NIHR01 DK094699
Record Number:CaltechAUTHORS:20170306-132431515
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74796
Deposited By: Ruth Sustaita
Deposited On:06 Mar 2017 21:34
Last Modified:24 Feb 2020 10:30

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