Glimma: Interactive HTML graphics
Version 1.4.0

This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.

AuthorShian Su, Matthew E. Ritchie, Charity Law, Stuart Lee
Bioconductor views DifferentialExpression GeneExpression Microarray RNASeq ReportWriting Sequencing Visualization
Date of publicationNone
MaintainerShian Su <su.s@wehi.edu.au>
LicenseGPL-3 | file LICENSE
Version1.4.0
URL https://github.com/Shians/Glimma
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Glimma")

Popular man pages

arraydata: Example microarray for the study of Ezh2.
glBar: Glimma MD Plot
glMDPlot: Glimma MD Plot
glMDPlot.DESeqResults: Glimma MD Plot
glScatter: Glimma Scatter Plot
is.hex: Hexcode colours
makeJson: JSON converter for R objects
See all...

All man pages Function index File listing

Man pages

arraydata: Example microarray for the study of Ezh2.
as.hexcol: Numeric to hex colour converter
glBar: Glimma MD Plot
glBar.default: Glimma MD Plot
glimma: Glimma plot manager
gllink: Plot linkages
glMDPlot: Glimma MD Plot
glMDPlot.default: Glimma MD Plot
glMDPlot.DESeqDataSet: Glimma MD Plot
glMDPlot.DESeqResults: Glimma MD Plot
glMDPlot.DGEExact: Glimma MD Plot
glMDPlot.DGELRT: Glimma MD Plot
glMDPlot.MArrayLM: Glimma MD Plot
glMDSPlot: Glimma MDS Plot
glMDSPlot.default: Glimma MDS Plot
glMDSPlot.DESeqDataSet: Glimma MDS Plot
glMDSPlot.DGEList: Glimma MDS Plot
glMDSPlot.SCESet: Glimma MDS Plot
glScatter: Glimma Scatter Plot
glScatter.default: Glimma Scatter Plot
glTable: Glimma Table
gltablink: Plot linkages
glXYPlot: Glimma XY Plot
is.hex: Hexcode colours
lymphomaRNAseq: Mouse based RNAseq data for study of smchd1 gene.
makeJson: JSON converter for R objects
makeJson.data.frame: JSON converter for data frames
makeJson.jschart: JSON converter for chart objects

Functions

arraydata Man page
arrayify Source code
as.hexcol Man page Source code
bsCol Source code
bsRowEnd Source code
bsRowStart Source code
char Source code
checkCountsAndSamples Source code
checkObjAnnoCountsShapes Source code
checkSideMainPresent Source code
checkThat Source code
constructBarPlot Source code
constructScatterPlot Source code
convertLogical Source code
convertStatusToCols Source code
draw.plots Source code
firstChar Source code
getCols Source code
getLabels Source code
getLogicalCols Source code
getRows Source code
glBar Man page Source code
glBar.default Man page Source code
glMDPlot Man page Source code
glMDPlot.DESeqDataSet Man page Source code
glMDPlot.DESeqResults Man page Source code
glMDPlot.DGEExact Man page
glMDPlot.DGELRT Man page Source code
glMDPlot.MArrayLM Man page Source code
glMDPlot.default Man page Source code
glMDSPlot Man page Source code
glMDSPlot.DESeqDataSet Man page Source code
glMDSPlot.DGEList Man page Source code
glMDSPlot.SCESet Man page Source code
glMDSPlot.default Man page Source code
glScatter Man page Source code
glScatter.default Man page Source code
glTable Man page Source code
glXYPlot Man page Source code
glimma Man page Source code
gllink Man page Source code
gltablink Man page Source code
hasCols Source code
hasLength Source code
hasRows Source code
initialiseGroups Source code
is.hex Man page Source code
isClass Source code
isFactor Source code
isIn Source code
isLogical Source code
isNumeric Source code
isString Source code
isType Source code
isUnique Source code
jsArgs Source code
jsCall Source code
jsChain Source code
jsFunction Source code
jsMethod Source code
lastChar Source code
lymphomaRNAseq Man page
makeAnno Source code
makeJson Man page Source code
makeJson.NULL Source code
makeJson.character Source code
makeJson.data.frame Man page Source code
makeJson.factor Source code
makeJson.jschart Man page Source code
makeJson.list Source code
makeJson.logical Source code
makeJson.numeric Source code
makeUnique Source code
naRowInds Source code
not.null Source code
notNull Source code
pathMaker Source code
plotWithTable Source code
printJsonToFile Source code
processPlot Source code
processTable Source code
quotify Source code
rmDuplicateCols Source code
sameAs Source code
sanitisePath Source code
setDisplayColumns Source code
sortInsigPointsToTop Source code
transformCounts Source code
writeMaker Source code

Files

.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R
R/checkThat.R
R/dataDoc.R
R/glBar.R
R/glMDPlot.R
R/glMDSPlot.R
R/glScatter.R
R/glTable.R
R/glXYPlot.R
R/glimma.R
R/gllink.R
R/gltablink.R
R/hexcol.R
R/jsHelper.R
R/jsonConvert.R
R/plotWithTable.R
R/textUtils.R
R/utilities.R
build
build/vignette.rds
data
data/arraydata.rda
data/datalist
data/lymphomaRNAseq.rda
inst
inst/NEWS
inst/css
inst/css/glimma.min.css
inst/css/src
inst/css/src/images
inst/css/src/images/animated-overlay.gif
inst/css/src/images/favicon.ico
inst/css/src/images/sort_asc.png
inst/css/src/images/sort_asc_disabled.png
inst/css/src/images/sort_both.png
inst/css/src/images/sort_desc.png
inst/css/src/images/sort_desc_disabled.png
inst/css/src/images/ui-bg_flat_0_aaaaaa_40x100.png
inst/css/src/images/ui-bg_flat_75_ffffff_40x100.png
inst/css/src/images/ui-bg_glass_55_fbf9ee_1x400.png
inst/css/src/images/ui-bg_glass_65_ffffff_1x400.png
inst/css/src/images/ui-bg_glass_75_dadada_1x400.png
inst/css/src/images/ui-bg_glass_75_e6e6e6_1x400.png
inst/css/src/images/ui-bg_glass_95_fef1ec_1x400.png
inst/css/src/images/ui-bg_highlight-soft_75_cccccc_1x100.png
inst/css/src/images/ui-icons_222222_256x240.png
inst/css/src/images/ui-icons_2e83ff_256x240.png
inst/css/src/images/ui-icons_454545_256x240.png
inst/css/src/images/ui-icons_888888_256x240.png
inst/css/src/images/ui-icons_cd0a0a_256x240.png
inst/doc
inst/doc/Glimma.R
inst/doc/Glimma.Rnw
inst/doc/Glimma.pdf
inst/index.html
inst/js
inst/js/glimma.min.js
man
man/arraydata.Rd
man/as.hexcol.Rd
man/glBar.Rd
man/glBar.default.Rd
man/glMDPlot.DESeqDataSet.Rd
man/glMDPlot.DESeqResults.Rd
man/glMDPlot.DGEExact.Rd
man/glMDPlot.DGELRT.Rd
man/glMDPlot.MArrayLM.Rd
man/glMDPlot.Rd
man/glMDPlot.default.Rd
man/glMDSPlot.DESeqDataSet.Rd
man/glMDSPlot.DGEList.Rd
man/glMDSPlot.Rd
man/glMDSPlot.SCESet.Rd
man/glMDSPlot.default.Rd
man/glScatter.Rd
man/glScatter.default.Rd
man/glTable.Rd
man/glXYPlot.Rd
man/glimma.Rd
man/gllink.Rd
man/gltablink.Rd
man/is.hex.Rd
man/lymphomaRNAseq.Rd
man/makeJson.Rd
man/makeJson.data.frame.Rd
man/makeJson.jschart.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/invalid_names_glMDPlot.RData
tests/testthat/little_mait_DGELRT.RData
tests/testthat/pasilla.RData
tests/testthat/test-checkThat.r
tests/testthat/test-glMDPlot.R
tests/testthat/test-glMDSPlot.R
tests/testthat/test-glXYPlot.R
tests/testthat/test-gllink.R
tests/testthat/test-hexcol.R
tests/testthat/test-jsonConvert.R
tests/testthat/test-textUtils.R
tests/testthat/test-utilities.R
tests/testthat/test_data_DESeqDataSet.RData
tests/testthat/test_data_DGEExact.RData
tests/testthat/test_data_DGELRT.RData
tests/testthat/test_data_MDS_DESeq.RData
tests/testthat/test_data_MDS_DGEList.RData
tests/testthat/test_data_voom.RData
tests/testthat/volcano_glXYPlot.RData
vignettes
vignettes/Glimma.Rnw
vignettes/GlimmaWorkFlow.png
vignettes/Glimma_plotlayout.png
vignettes/MDSarray.png
vignettes/MDSgroups.png
vignettes/MDage.png
vignettes/MDanno.png
vignettes/MDarray.png
vignettes/XYarray.png
vignettes/XYvolcano.png
vignettes/quickstart_md.png
vignettes/quickstart_mds.png
Glimma documentation built on May 20, 2017, 11 p.m.

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