README.md

In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

SCISSOR

Shape Changes In Selecting Sample Outliers in RNA-seq

Overview

SCISSOR (shape changes in selecting sample outliers in RNA-seq) aims for unsupervised screening of a range of structural alterations in RNA-seq data. SCISSOR considers a novel shape property of aligned short read data through a base-level pileup file. This intact and uncompressed view of RNA-seq profile enables the unbiased discovery of structural alterations by looking for anomalous shapes in expression. This approach holds promise for identifying otherwise obscured genetic aberrations. As a result, SCISSOR identifies known as well as novel aberrations including abnormal splicing, intra-/intergenic deletions, small indels, alternative transcription start/termination.

Documentation

The documentation is available at https://hyochoi.github.io/SCISSOR

System Requirements

This package has been tested on the following systems:

• macOS: Mojave (10.14.6)
• Linux: CentOS (7.5)

R package dependencies

SCISSOR requires the following packages:

• BiocManager
• Rsamtools
• GenomicRanges
• refGenome
• RColorBrewer
• wesanderson
• nloptr
• zoo

Installation Guide

1. install devtools:

if ("devtools" %in% rownames(installed.packages()) == FALSE) {install.packages("devtools")}
library(devtools)

1. install SCISSOR:

install_github("hyochoi/SCISSOR")
library(SCISSOR)

Installation takes 5-10 mins.

Note:

If you see errors like the following:

‘rlang’ 0.3.4 is already loaded, but >= 0.4.0 is required

try this:

devtools::install_github("r-lib/rlang", build_vignettes = TRUE)

hyochoi/SCISSOR documentation built on July 6, 2022, 6:59 a.m.