CRAN/E | bulkAnalyseR

bulkAnalyseR

Interactive Shiny App for Bulk Sequencing Data

Installation

About

Given an expression matrix from a bulk sequencing experiment, pre-processes it and creates a shiny app for interactive data analysis and visualisation. The app contains quality checks, differential expression analysis, volcano and cross plots, enrichment analysis and gene regulatory network inference, and can be customised to contain more panels by the user.

github.com/Core-Bioinformatics/bulkAnalyseR
Bug report File report

Key Metrics

Version 1.1.0
R ≥ 4.0
Published 2022-12-15 492 days ago
Needs compilation? no
License GPL-2
CRAN checks bulkAnalyseR results

Downloads

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Maintainer

Maintainer

Ilias Moutsopoulos

im383@cam.ac.uk

Authors

Ilias Moutsopoulos

aut / cre

Eleanor Williams

aut / ctb

Irina Mohorianu

aut / ctb

Material

README
Reference manual
Package source

Vignettes

A beginner's guide to creating a bulkAnalyseR app from a GEO dataset
bulkAnalyseR: Integrating multi-omics or external data
bulkAnalyseR: An accessible, interactive pipeline for analysing and sharing bulk sequencing results

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

bulkAnalyseR archive

Depends

R ≥ 4.0

Imports

ggplot2
shiny
gprofiler2
edgeR
DESeq2
stats
ggrepel
utils
RColorBrewer
ComplexHeatmap
circlize
grid
shinyWidgets
shinyjqui
dplyr
magrittr
ggforce
rlang
glue
preprocessCore
matrixStats
noisyr
tibble
ggnewscale
ggrastr
GENIE3
visNetwork
DT
scales
shinyjs
tidyr
shinyLP
UpSetR
stringr
ggVennDiagram

Suggests

rmarkdown
knitr
shinythemes
BiocManager
AnnotationDbi
org.Hs.eg.db
org.Mm.eg.db
readxl
testthat ≥ 3.0.0