ganalyse: ganalyse: Easy Analysis of Genomics Data

In openanalytics/ganalyse: Easy Analysis of RNASeq DE

Description

ganalyse is an R package that aims to make analysis on genomics data easy. It is implemented only for RNA-Seq data at the moment.

Details

The current organisation is as follows:

• Provide experiment, sample_info and format to the function rnaseq to generate an object of class fpkm or raw.

• Collect counts using gather_counts to load the corresponding count data for the samples. It returns an object of class fpkm_counts or raw_counts respectively.

• Construct design matrix and contrasts. See construct_design and construct_contrasts.

• Perform different types on analyses (only Differential Gene Expression (DGE) analysis is supported currently) on the fpkm_counts or raw_counts object.

  For fpkm_counts object, use limma_dge to perform DGE analysis. Similarly, for raw_counts object, use limma_dge or edger_dge methods.

Note

The term differential gene expression or DGE is not used in a restrictive manner and applies to genomic features in general, i.e., genes, transcripts, exons etc.

See Also

rnaseq gather_counts show_counts construct_design construct_contrasts limma_dge edger_dge as.eset

openanalytics/ganalyse documentation built on May 24, 2019, 2:25 p.m.