README.md

In Oshlack/Baller: Classification of RNA-seq data from ALL samples

And we're updating this... But stick around here for the old version! The new ALLSorts can be found here: https://github.com/Oshlack/AllSorts.

Welcome to the All Sorts Readme!

AllSorts is a B-Cell Acute Lymphoblastic Leukemia Classifier, aiming to classify ALL into its various sub-types using RNA-Seq data to observe gene expression profiles.

The tool is an R package which includes vignettes for you to peruse at your own pace which will explain how to use the classifier.

Installation

To install an R package from GitHub, first you will need to install the devtools packge. So open an R/RStudio session:

install.packages("devtools")

Load the devtools package.

library(devtools)

Then simply use the install_github("author/package") function of devtools. So for AllSorts that would simply be:

install_github("Oshlack/AllSorts_v1")

Alternatively if one does not have the required BioConductor packages such as edgeR/limma one may wish to install using BiocLite. Note devtools are still required in this case.

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Oshlack/AllSorts")

Manual/Tutorial

To read the manual please read the R vignette after installing the pacakge for the most up-to-date manual and tutorial, alternatively read the package wiki.

https://github.com/Oshlack/AllSorts/wiki

Oshlack/Baller documentation built on Jan. 23, 2021, 6:50 p.m.