https://github.com/jackhump/cryptex
Scripts used to discover and quantify non-annotated cryptic splicing in RNA-seq data
https://github.com/jackhump/cryptex
Last synced: 5 months ago
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Scripts used to discover and quantify non-annotated cryptic splicing in RNA-seq data
- Host: GitHub
- URL: https://github.com/jackhump/cryptex
- Owner: jackhump
- Created: 2016-08-10T12:36:56.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2017-09-07T17:18:19.000Z (almost 9 years ago)
- Last Synced: 2023-07-31T21:25:26.686Z (almost 3 years ago)
- Language: R
- Homepage:
- Size: 112 KB
- Stars: 1
- Watchers: 1
- Forks: 2
- Open Issues: 2
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Metadata Files:
- Readme: README.md
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README
# CryptEx
A set of scripts that identify, quantify and classify cryptic splicing in RNA-seq data.
CryptEx paper is now published!
## Quantitative analysis of cryptic splicing associated with TDP-43 depletion
### Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs and Vincent Plagnol
https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-017-0274-1
## Pre-requisites:
* BEDTools
* R (>= 3.1)
* SAMtools
* STAR - to align fastq files and generate splice junctions
### R packages:
* BioStrings
* DEXSeq
* data.table
* dplyr
* GenomicRanges
* ggplot2
* gridExtra
* gplot
* optparse
* plyr
* stringr
* tidyr