crossmeta

DOI:10.18129/B9.bioc.crossmeta

This is thedevelopmentversion of crossmeta; for the stable release version, seecrossmeta.

Cross Platform Meta-Analysis of Microarray Data

Bioconductor version: Development (3.16)

Implements cross-platform and cross-species meta-analyses of Affymentrix, Illumina, and Agilent microarray data. This package automates common tasks such as downloading, normalizing, and annotating raw GEO data. The user then selects control and treatment samples in order to perform differential expression analyses for all comparisons. After analysing each contrast seperately, the user can select tissue sources for each contrast and specify any tissue sources that should be grouped for the subsequent meta-analyses.

Author: Alex Pickering

Maintainer: Alex Pickering

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("crossmeta")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("crossmeta")

HTML	R Script	crossmeta vignette
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Annotation,BatchEffect,DifferentialExpression,GUI,GeneExpression,Microarray,OneChannel,Preprocessing,Software,TissueMicroarray,Transcription
Version	1.23.3
In Bioconductor since	BioC 3.4 (R-3.3) (5.5 years)
License	MIT + fileLICENSE
Depends	R (>= 4.0)
Imports	affy(>= 1.52.0),affxparser(>= 1.46.0),AnnotationDbi(>= 1.36.2),Biobase(>= 2.34.0),BiocGenerics(>= 0.20.0),BiocManager(>= 1.30.4),DT(>= 0.2),DBI(>= 1.0.0),data.table(>= 1.10.4),edgeR,fdrtool(>= 1.2.15),GEOquery(>= 2.40.0),limma(>= 3.30.13),matrixStats(>= 0.51.0),metaMA(>= 3.1.2),miniUI(>= 0.1.1), methods,oligo(>= 1.38.0),reader(>= 1.0.6),RCurl(>= 1.95.4.11),RSQLite(>= 2.1.1),stringr(>= 1.2.0),sva(>= 3.22.0),shiny(>= 1.0.0),shinyjs(>= 2.0.0),shinyBS(>= 0.61),shinyWidgets(>= 0.5.3),shinypanel(>= 0.1.0),tibble,XML(>= 3.98.1.17),readxl(>= 1.3.1)
LinkingTo
Suggests	knitr,rmarkdown,lydata,org.Hs.eg.db,testthat
SystemRequirements	libxml2: libxml2-dev (deb), libxml2-devel (rpm) libcurl: libcurl4-openssl-dev (deb), libcurl-devel (rpm) openssl: libssl-dev (deb), openssl-devel (rpm), libssl_dev (csw), openssl@1.1 (brew)
Enhances
URL	https://github.com/alexvpickering/crossmeta
BugReports	https://github.com/alexvpickering/crossmeta/issues
Depends On Me
Imports Me
Suggests Me	ccmap
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 指示在R会话中使用这个包.

Source Package	crossmeta_1.23.3.tar.gz
Windows Binary	crossmeta_1.23.3.zip
macOS 10.13 (High Sierra)	crossmeta_1.23.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/crossmeta
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/crossmeta
Package Short Url	//www.andersvercelli.com/packages/crossmeta/
Package Downloads Report	Download Stats