bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data

Abstract Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art appro...

Full description

Saved in:
Bibliographic Details
Published in:Briefings in bioinformatics 2023-01, Vol.24 (1)
Main Authors: Moutsopoulos, Ilias, Williams, Eleanor C, Mohorianu, Irina I
Format: Article
Language:English
Subjects:
Accessibility
Image quality
Multiomics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Abstract Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art approaches using an expression matrix as the starting point (pre-processing functions are available as part of the package). Static summary images are replaced with interactive panels illustrating quality-checking, differential expression analysis (with noise detection) and biological interpretation (enrichment analyses, identification of expression patterns, followed by inference and comparison of regulatory interactions). bulkAnalyseR can handle different modalities, facilitating robust integration and comparison of cis-, trans- and customised regulatory networks.
ISSN:1467-5463
1477-4054
DOI:10.1093/bib/bbac591