Genominator: Analyze, manage and store genomic data

Tools for storing, accessing, analyzing and visualizing genomic data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Genominator")
AuthorJames Bullard, Kasper Daniel Hansen
Bioconductor views Infrastructure
Date of publicationNone
MaintainerJames Bullard <bullard@stat.berkeley.edu>
LicenseArtistic-2.0
Version1.30.0

View on Bioconductor

Functions

addPrimingWeights Man page
aggregateExpData Man page
applyMapped Man page
chr1_yeast Man page
collapseExpData Man page
computeCoverage Man page
computePrimingWeights Man page
ExpData Man page
ExpData-class Man page
[,ExpData-method Man page
$,ExpData-method Man page
Genominator Man page
Genominator-package Man page
getColnames Man page
getDBConnection Man page
getDBFilename Man page
getIndexColumns Man page
getMode Man page
getRegion Man page
getSchema Man page
getTablename Man page
head,ExpData-method Man page
importFromAlignedReads Man page
importToExpData Man page
initialize,ExpData-method Man page
joinExpData Man page
listTables Man page
makeGeneRepresentation Man page
mergeWithAnnotation Man page
plot.genominator.coverage Man page
plot.genominator.goodness.of.fit Man page
regionGoodnessOfFit Man page
regionGoodnessOfFit,data.frame-method Man page
regionGoodnessOfFit,ExpData-method Man page
regionGoodnessOfFit-methods Man page
show,ExpData-method Man page
splitByAnnotation Man page
summarizeByAnnotation Man page
summarizeExpData Man page
validAnnotation Man page
yeastAnno Man page
yeastAnno.sources Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Genominator.R R/annotation.R R/coverage.R R/diffExp.R R/emZero.R R/goodnessOfFit.R R/importAndManage.R R/plotRegion.R R/primingWeights.R
TODO
build
build/vignette.rds
data
data/chr1_yeast.rda
data/yeastAnno.rda
data/yeastAnno.sources.rda
inst
inst/CITATION
inst/benchmark
inst/benchmark/idxTiming.R
inst/doc
inst/doc/Genominator.R
inst/doc/Genominator.Rnw
inst/doc/Genominator.pdf
inst/doc/plotting.R
inst/doc/plotting.Rnw
inst/doc/plotting.pdf
inst/doc/withShortRead.R
inst/doc/withShortRead.Rnw
inst/doc/withShortRead.pdf
inst/sample.db
inst/scripts
inst/scripts/consistency.txt
inst/scripts/import-marioni.sh
inst/scripts/pipeline-marioni.R
inst/scripts/pipeline-marioni.sh
inst/scripts/pipeline-yeast1.sh
inst/scripts/pipeline.sh
inst/scripts/reshape-marioni.pl
inst/scripts/reshape-yeast1.pl
inst/scripts/sqlimport.sh
inst/scripts/temp.R
man
man/ExpData.Rd man/Genominator.Rd man/addPrimingWeights.Rd man/aggregateExpData.Rd man/applyMapped.Rd man/collapseExpData.Rd man/computeCoverage.Rd man/computePrimingWeights.Rd man/getRegion.Rd man/importFromAlignedReads.Rd man/importToExpData.Rd man/joinExpData.Rd man/makeGeneRepresentation.Rd man/mergeWithAnnotation.Rd man/plot.genominator.coverage.Rd man/plot.genominator.goodness.of.fit.Rd man/regionGoodnessOfFit-methods.Rd man/splitByAnnotation.Rd man/summarizeByAnnotation.Rd man/summarizeExpData.Rd man/validAnnotation.Rd man/yeastAnno.Rd
tests
tests/runTests.R_test
tests/testDiffExp.R_test
tests/testEM.R_test
tests/testGenominatorFxs.R_test
tests/testGoodnessOfFit.R_test
tests/testHasOverlap.R_test
tests/testImport.R_test
vignettes
vignettes/Genominator.Rnw
vignettes/plotting.Rnw
vignettes/withShortRead.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.