Genominator: Analyze, manage and store genomic data

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

AuthorJames Bullard, Kasper Daniel Hansen
Date of publicationNone
MaintainerJames Bullard <bullard@stat.berkeley.edu>
LicenseArtistic-2.0
Version1.28.0

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

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