crossmeta: Cross Platform Meta-Analysis of Microarray Data

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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. A user interface makes it easy to select control and treatment samples for each contrast and study. This input is used for subsequent surrogate variable analysis (models unaccounted sources of variation) and differential expression analysis. Final meta-analysis of differential expression values can include genes measured in only a subset of studies.

Author
Alex Pickering
Date of publication
None
Maintainer
Alex Pickering <alexvpickering@gmail.com>
License
MIT + file LICENSE
Version
1.0.1

View on Bioconductor

Man pages

contribute
Contribute results of meta-analysis to public database.
diff_expr
Differential expression of esets.
es_meta
Effect size combination meta anaylsis.
get_raw
Download and unpack microarray supplementary files from GEO.
load_diff
Load previous differential expression analysis.
load_raw
Load and annotate raw data downloaded from GEO.
open_raw_illum
Open raw Illumina microarray files.
setup_prev
Setup selections when many samples.
symbol_annot
Add hgnc symbol to expression set.

Files in this package

crossmeta/DESCRIPTION
crossmeta/LICENSE
crossmeta/NAMESPACE
crossmeta/R
crossmeta/R/diff_utils.R
crossmeta/R/load_affy.R
crossmeta/R/load_agil.R
crossmeta/R/load_illum.R
crossmeta/R/load_utils.R
crossmeta/R/meta_utils.R
crossmeta/R/selection_utils.R
crossmeta/R/setup_prev.R
crossmeta/R/sysdata.rda
crossmeta/README.md
crossmeta/build
crossmeta/build/vignette.rds
crossmeta/inst
crossmeta/inst/doc
crossmeta/inst/doc/crossmeta-vignette.R
crossmeta/inst/doc/crossmeta-vignette.Rmd
crossmeta/inst/doc/crossmeta-vignette.html
crossmeta/man
crossmeta/man/contribute.Rd
crossmeta/man/diff_expr.Rd
crossmeta/man/es_meta.Rd
crossmeta/man/get_raw.Rd
crossmeta/man/load_diff.Rd
crossmeta/man/load_raw.Rd
crossmeta/man/open_raw_illum.Rd
crossmeta/man/setup_prev.Rd
crossmeta/man/symbol_annot.Rd
crossmeta/tests
crossmeta/tests/testthat
crossmeta/tests/testthat.R
crossmeta/tests/testthat/test-all.R
crossmeta/vignettes
crossmeta/vignettes/crossmeta-vignette.Rmd