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This is the development version of crossmeta; for the stable release version, see crossmeta.
Bioconductor version: Development (3.18)
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 <alexvpickering at gmail.com>
Citation (from within R,
enter citation("crossmeta")
):
To install this package, start R (version "4.3") 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 appropriate Bioconductor release.
Reference Manual |
biocViews | Annotation, BatchEffect, DifferentialExpression, GUI, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription |
Version | 1.27.0 |
In Bioconductor since | BioC 3.4 (R-3.3) (6.5 years) |
License | MIT + file LICENSE |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | |
Windows Binary | crossmeta_1.27.0.zip |
macOS Binary (x86_64) | crossmeta_1.27.0.tgz |
macOS Binary (arm64) | |
Source Repository | git clone https://git.bioconductor.org/packages/crossmeta |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/crossmeta |
Bioc Package Browser | https://code.bioconductor.org/browse/crossmeta/ |
Package Short Url | https://bioconductor.org/packages/crossmeta/ |
Package Downloads Report | Download Stats |
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