ImmuneSpaceR: A Thin Wrapper around the ImmuneSpace Database
Version 1.4.0

Provides a convenient API for accessing data sets within ImmuneSpace (www.immunespace.org), the data repository and analysis platform of the Human Immunology Project Consortium (HIPC).

AuthorGreg Finak, Renan Sauteraud, Mike Jiang, Gil Guday, Leo Dashevskiy, Evan Henrich, Ju Yeong Kim
Bioconductor views DataImport DataRepresentation ThirdPartyClient
Date of publicationNone
MaintainerImmuneSpace Package Maintainer <immunespace@gmail.com>
LicenseGPL-2
Version1.4.0
URL https://github.com/RGLab/ImmuneSpaceR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ImmuneSpaceR")

Getting started

Package overview
README.md
Abundance of plasmablasts measured by multiparameter flow cytometry in SDY180
A simple introduction to the ImmuneSpaceR package
Correlating HAI with flow cytometry and ELISPOT results in SDY269
Correlation of HAI/virus neutralizition titer and cell counts in SDY144
Downloading expression matrices using ImmuneSpaceR
getDataset

Popular man pages

check_netrc: Check netrc file
ImmuneSpaceConnection-class: The ImmuneSpaceConnection class
ImmuneSpaceR-package: A Thin Wrapper Around ImmuneSpace
loadConnection: Save/Load an ImmuneSpaceConnection object from disk
template_IS: template_IS
theme_IS: theme_IS
write_netrc: Write a netrc file
See all...

All man pages Function index File listing

Man pages

check_netrc: Check netrc file
CreateConnection: CreateConnection
ImmuneSpaceConnection-class: The ImmuneSpaceConnection class
ImmuneSpaceR-package: A Thin Wrapper Around ImmuneSpace
ISpalette: ImmuneSpace palette
loadConnection: Save/Load an ImmuneSpaceConnection object from disk
template_IS: template_IS
theme_IS: theme_IS
write_netrc: Write a netrc file

Functions

.ISCon Man page
CreateConnection Man page Source code Source code
EMNames Man page
ISpalette Man page Source code
ImmuneSpace Man page
ImmuneSpaceConnection Man page
ImmuneSpaceConnection-class Man page
ImmuneSpaceR Man page
ImmuneSpaceR-package Man page
addTrt Man page
check_filter Source code
check_netrc Man page Source code
combineEMs Source code
filterDT Source code
filter_cached_copy Source code
format_lab Source code
getDataToPlot Source code
getDataset Man page
getGEAnalysis Man page
getGEMatrix Man page
heatmapAnnotations Source code
listDatasets Man page
listGEAnalysis Man page
loadConnection Man page Source code
onLoad Source code
override_scale Source code
qpBoxplotViolin Source code
qpHeatmap2 Source code
qpLineplot Source code
quick_plot Man page Source code
saveConnection Man page Source code
standardize_time Source code
template_IS Man page Source code
theme_IS Man page Source code
write_netrc Man page Source code

Files

.travis.yml
DESCRIPTION
NAMESPACE
R
R/CreateConnection.R
R/ImmuneSpace.R
R/ImmuneSpaceR.R
R/getDataset.R
R/getGEMatrix.R
R/netrc.R
R/quick_plot.R
R/utils.R
R/zzz.R
README.md
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/Using_RImmuneSpace.R
inst/doc/Using_RImmuneSpace.Rmd
inst/doc/Using_RImmuneSpace.html
inst/doc/arrays.R
inst/doc/arrays.Rmd
inst/doc/arrays.html
inst/doc/getDataset.R
inst/doc/getDataset.Rmd
inst/doc/getDataset.html
inst/doc/report_SDY144.R
inst/doc/report_SDY144.Rmd
inst/doc/report_SDY144.html
inst/doc/report_SDY180.R
inst/doc/report_SDY180.Rmd
inst/doc/report_SDY180.html
inst/doc/report_SDY269.R
inst/doc/report_SDY269.Rmd
inst/doc/report_SDY269.html
inst/extdata
inst/extdata/saved_con.rds
inst/img
inst/img/qpHai.png
inst/rmarkdown
inst/rmarkdown/templates
inst/rmarkdown/templates/ImmuneSpace
inst/rmarkdown/templates/ImmuneSpace/resources
inst/rmarkdown/templates/ImmuneSpace/resources/IStemplate.css
inst/rmarkdown/templates/ImmuneSpace/resources/IStemplate.scss
inst/rmarkdown/templates/ImmuneSpace/resources/git-pre-commit-hook
inst/rmarkdown/templates/ImmuneSpace/resources/labkey-logo.png
inst/rmarkdown/templates/ImmuneSpace/skeleton
inst/rmarkdown/templates/ImmuneSpace/skeleton/skeleton.Rmd
inst/rmarkdown/templates/ImmuneSpace/template.yaml
inst/ssl_certs
inst/ssl_certs/README.txt
inst/ssl_certs/ca-bundle.crt
inst/testthat
man
man/CreateConnection.Rd
man/ISpalette.Rd
man/ImmuneSpaceConnection-class.Rd
man/ImmuneSpaceR-package.Rd
man/check_netrc.Rd
man/loadConnection.Rd
man/template_IS.Rd
man/theme_IS.Rd
man/write_netrc.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/global_variable.R
tests/testthat/test-framework.R
vignettes
vignettes/Using_RImmuneSpace.Rmd
vignettes/arrays.Rmd
vignettes/getDataset.Rmd
vignettes/img
vignettes/img/getDataset-views.png
vignettes/report_SDY144.Rmd
vignettes/report_SDY180.Rmd
vignettes/report_SDY269.Rmd
ImmuneSpaceR documentation built on May 20, 2017, 10:52 p.m.

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