In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

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bbcRNA: An R package for facilitating RNA-Seq analysis

The goal of bbcRNA is to facilitate RNA-seq analysis, starting from counts and ending with differentially expressed gene lists and enerichment analyses. The major feature are classes to store different parts of the RNA-Seq analysis and wrapper functions for running popular tools such as EdgeR and ClusterProfiler. See the bbcRNA website for a built vignette.

Installation

You can install bbcRNA from GitHub with:

if (!requireNamespace("devtools", quietly = TRUE))
  install.packages("devtools")

devtools::install_github("vari-bbc/bbcRNA")

New classes defined in the bbcRNA package

New classes have been defined to enable more convenient storage of different parts of a DE analysis.

The BbcSE class

The BbcSE class extends SummarizedExperiment. Additional slots are:

1. aln_metrics: a matrix containing alignment metrics for samples.
2. edger : a BbcEdgeR object.
3. deseq2: For storing DESeqDataSet and DESeqResults; not implemented yet.

The BbcEdgeR class

Slots are:

1. dgelist: a DGEList object.
2. de_results: a list. First element is always a DGEGLM object. The others are edgeR result objects.
3. norm_cts: a SummarizedExperiment object for storing normalized counts.

Usage

# attach the package
library(bbcRNA)

# run the BbcSE constructor without any data to show the structure 
BbcSE()

# run the BbcEdgeR constructor without any data to show the structure 
BbcEdgeR()

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.