Files in malnirav/hiReadsProcessor
Functions to process LM-PCR reads from 454/Illumina data
.BBSoptions
.Rbuildignore
.Rinstignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/hiReadsProcessor.R
README.md
data/FLX_seqProps.RData
data/psl.RData
hiReadsProcessor.Rproj
inst/extdata/FLX_sample_run/RunData/1.TCA.454Reads.fna
inst/extdata/FLX_sample_run/RunData/1.TCA.454Reads.fna.gz
inst/extdata/FLX_sample_run/RunData/2.TCA.454Reads.fna
inst/extdata/FLX_sample_run/RunData/2.TCA.454Reads.fna.gz
inst/extdata/FLX_sample_run/RunData/3.TCA.454Reads.fna
inst/extdata/FLX_sample_run/RunData/3.TCA.454Reads.fna.gz
inst/extdata/FLX_sample_run/Vectors/HIV1.fa
inst/extdata/FLX_sample_run/Vectors/MLV-vector.fa
inst/extdata/FLX_sample_run/sampleInfo.xls
inst/extdata/FLX_sample_run/sampleInfo.xlsx
inst/tests/runTests.R
inst/tests/tests/test_coreFeatures.R
man/addFeature.Rd
man/addListNameToReads.Rd
man/annotateSites.Rd
man/blatListedSet.Rd
man/blatSeqs.Rd
man/chunkize.Rd
man/clusterSites.Rd
man/crossOverCheck.Rd
man/dereplicateReads.Rd
man/doRCtest.Rd
man/extractFeature.Rd
man/extractSeqs.Rd
man/findAndRemoveVector.Rd
man/findAndTrimSeq.Rd
man/findBarcodes.Rd
man/findIntegrations.Rd
man/findLTRs.Rd
man/findLinkers.Rd
man/findPrimers.Rd
man/findVector.Rd
man/getIntegrationSites.Rd
man/getSectorsForSamples.Rd
man/getSonicAbund.Rd
man/hiReadsProcessor.Rd
man/isuSites.Rd
man/otuSites.Rd
man/pairUpAlignments.Rd
man/pairwiseAlignSeqs.Rd
man/primerIDAlignSeqs.Rd
man/psl.Rd
man/pslCols.Rd
man/pslToRangedObject.Rd
man/read.BAMasPSL.Rd
man/read.SeqFolder.Rd
man/read.blast8.Rd
man/read.psl.Rd
man/read.sampleInfo.Rd
man/read.seqsFromSector.Rd
man/removeReadsWithNs.Rd
man/replicateReads.Rd
man/sampleSummary.Rd
man/seqProps.Rd
man/splitByBarcode.Rd
man/splitSeqsToFiles.Rd
man/startgfServer.Rd
man/trimSeqs.Rd
man/troubleshootLinkers.Rd
man/vpairwiseAlignSeqs.Rd
man/write.listedDNAStringSet.Rd
man/write.psl.Rd
tests/testthat/runTests.R
tests/testthat/test_coreFeatures.R
vignettes/Tutorial.R
vignettes/Tutorial.Rmd
vignettes/Tutorial.html
vignettes/Tutorial.md
vignettes/hiReadsProcessor_object.png
vignettes/hiReadsProcessor_workflow.png
