Genominator: Analyze, manage and store genomic data

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

Author
James Bullard, Kasper Daniel Hansen
Date of publication
None
Maintainer
James Bullard <bullard@stat.berkeley.edu>
License
Artistic-2.0
Version
1.28.0

View on Bioconductor

Man pages

addPrimingWeights
Adding priming weights to an AlignedRead object.
aggregateExpData
Collapse data into unique entries
applyMapped
Apply a function over mapped data.
collapseExpData
Combine multiple data sets
computeCoverage
Compute effort-coverage values
computePrimingWeights
Compute weights to correct for random hexamer priming.
ExpData
Class "ExpData"
Genominator
Data backend for Genomic data
getRegion
Select a region from an ExpData object.
importFromAlignedReads
Import aligned reads to database
importToExpData
Import data to database
joinExpData
Merge ExpData objects
makeGeneRepresentation
Compute a gene representation from annotation.
mergeWithAnnotation
Combine data with annotation
plot.genominator.coverage
Create coverage plot
plot.genominator.goodness.of.fit
Create goodness-of-fit quantile-quantile plot
regionGoodnessOfFit-methods
Calculate goodness-of-fit statistics
splitByAnnotation
Split data into a list by annotation element.
summarizeByAnnotation
Summarize data based on genome annotation.
summarizeExpData
Summarize a data column
validAnnotation
Check for validity of a annotation object.
yeastAnno
Example datasets from Genominator

Files in this package

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