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Keep Me Around (kma): Intron Retention Detection

kma is an R package that performs intron retention estimation and detection using biological replicates and resampling. Updated code can always be found at https://github.com/pachterlab/kma

Installation

To install, first ensure you have the required packages:

required_packages <- c("devtools", "data.table", "reshape2", "dplyr")
install.packages(required_packages)

You can then install the package using devtools:

devtools::install_github("pachterlab/kma")

Assuming all goes well, load kma:

library("kma")

Tutorial

After it has been installed, please see the vignette in R:

vignette("kma")

Bugs and feature requests

Please file these on Github.

Future work

  • Additional exploratory analysis plotting tools
  • Provide differential intron usage analysis between experimental conditions
    • We currently have some ideas on how to do this and will likely be implementing it soon
  • Provide time series analysis

Authors

Software was developed by Harold Pimentel. Methods were developed with Lior Pachter and John Conboy.

Related open source tools

Below you will find a list of related tools and how they differ from kma.

DEXSeq

DEXSeq is interested in differential usage across genic regions. As a result, it does not determine whether an intron is being "used" (relative to transript expression), simply that it is being "differentially used."

MISO

MISO can calculate the intronic percent spliced in (PSI), though it currently requires a modified annotation from their website. kma can currently work with any annotation, as the annotation will be processed during the pre-processing step. Also, MISO does not currently provide built-in suppport for replicates.