hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data
Version 1.12.0

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

AuthorNirav V Malani <malnirav@gmail.com>
Bioconductor views Preprocessing Sequencing
Date of publicationNone
MaintainerNirav V Malani <malnirav@gmail.com>
LicenseGPL-3
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("hiReadsProcessor")

Getting started

README.md

Popular man pages

findAndRemoveVector: Find and trim vector sequence from reads.
findAndTrimSeq: Find and trim a short pattern sequence from the subject.
getSonicAbund: Calculate breakpoint/sonic abundance of integration sites in...
primerIDAlignSeqs: Align a short pattern with PrimerID to variable length target...
read.BAMasPSL: Reads a BAM/SAM file and converts it into a PSL like format.
read.blast8: Read blast8 file(s) outputted by BLAT
startgfServer: Start/Stop a gfServer instance
See all...

All man pages Function index File listing

Man pages

addFeature: Add a specific feature/attribute to the sampleInfo object.
addListNameToReads: Prepend name attribute of a list to DNAStringSet
annotateSites: Find the 5' primers and add results to SampleInfo object.
blatListedSet: Align a listed DNAStringSet to a reference using gfClient or...
blatSeqs: Align sequences using BLAT.
chunkize: Breaks an object into chunks of N size.
clusterSites: Cluster/Correct values within a window based on their...
crossOverCheck: Remove values/positions which are overlapping between...
dereplicateReads: Removes duplicate sequences from DNAStringSet object.
doRCtest: Test if pattern aligns better in +/- orientation.
extractFeature: Extract a specific feature/attribute of the sampleInfo...
extractSeqs: Extract sequences for a feature in the sampleInfo object.
findAndRemoveVector: Find and trim vector sequence from reads.
findAndTrimSeq: Find and trim a short pattern sequence from the subject.
findBarcodes: Demultiplex reads by their barcodes
findIntegrations: Find the integration sites and add results to SampleInfo...
findLinkers: Find the 3' linkers and add results to SampleInfo object.
findLTRs: Find the 5' LTRs and add results to SampleInfo object.
findPrimers: Find the 5' primers and add results to SampleInfo object.
findVector: Find vector DNA in reads and add results to SampleInfo...
getIntegrationSites: Obtain integration sites from BLAT output
getSectorsForSamples: Get sectors for samples defined in the sampleInfo object.
getSonicAbund: Calculate breakpoint/sonic abundance of integration sites in...
hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data
isuSites: Bin values or make ISUs by assigning a unique ID to them...
otuSites: Bin values or make OTUs by assigning a unique ID to them...
pairUpAlignments: Pair up alignments in a GRanges object
pairwiseAlignSeqs: Align a short pattern to variable length target sequences.
primerIDAlignSeqs: Align a short pattern with PrimerID to variable length target...
psl: PSL file output
pslCols: Return PSL file columns with classes
pslToRangedObject: Convert psl dataframe to GRanges
read.BAMasPSL: Reads a BAM/SAM file and converts it into a PSL like format.
read.blast8: Read blast8 file(s) outputted by BLAT
read.psl: Read PSL file(s) outputted by BLAT
read.sampleInfo: Read a sample information file and format appropriate...
read.SeqFolder: Read contents of a sequencing folder and make a SimpleList...
read.seqsFromSector: Read fasta/fastq/sff given the path or sampleInfo object.
removeReadsWithNs: Remove sequences with ambiguous nucleotides.
replicateReads: Replicate sequences from DNAStringSet object using counts...
sampleSummary: Simple summary of a sampleInfo object.
seqProps: Sample Integration Sites Sequencing Data
splitByBarcode: Split DNAStringSet object using first X number of bases...
splitSeqsToFiles: Split DNA sequences into smaller files.
startgfServer: Start/Stop a gfServer instance
trimSeqs: Trim sequences from a specific side.
troubleshootLinkers: Compare LTRed/Primed sequences to all linkers.
vpairwiseAlignSeqs: Align a short pattern to variable length target sequences.
write.listedDNAStringSet: Write a fasta file per sample in parallel
write.psl: Write PSL file from dataframe or GRanges

Functions

addFeature Man page Source code
addListNameToReads Man page Source code
annotateSites Man page Source code
blatListedSet Man page Source code
blatSeqs Man page Source code
checkArgsSetDefaults_ALIGNed Source code
checkArgs_SEQed Source code
chunkize Man page Source code
clusterSites Man page Source code
crossOverCheck Man page Source code
decodeByBarcode Man page
dereplicateReads Man page Source code
doRCtest Man page Source code
extractFeature Man page Source code
extractSeqs Man page Source code
findAndRemoveVector Man page Source code
findAndTrimSeq Man page Source code
findBarcodes Man page Source code
findIntegrations Man page Source code
findLTRs Man page Source code
findLinkers Man page Source code
findPrimers Man page Source code
findVector Man page Source code
getIntegrationSites Man page Source code
getSectorsForSamples Man page Source code
getSonicAbund Man page Source code
hiReadsProcessor Man page
hiReadsProcessor-package Man page
isuSites Man page Source code
otuSites Man page Source code
pairUpAlignments Man page Source code
pairwiseAlignSeqs Man page Source code
primerIDAlignSeqs Man page Source code
psl Man page
pslCols Man page Source code
pslToRangedObject Man page Source code
read.BAMasPSL Man page Source code
read.SeqFolder Man page Source code
read.blast8 Man page Source code
read.psl Man page Source code
read.sampleInfo Man page Source code
read.seqsFromSector Man page Source code
removeReadsWithNs Man page Source code
replicateReads Man page Source code
sampleSummary Man page Source code
seqProps Man page
showFindStats Source code
splitByBarcode Man page Source code
splitSeqsToFiles Man page Source code
startgfServer Man page Source code
stopgfServer Man page Source code
trimSeqs Man page Source code
troubleshootLinkers Man page Source code
uniqueLength Source code
vpairwiseAlignSeqs Man page Source code
write.listedDNAStringSet Man page Source code
write.psl Man page Source code

Files

.BBSoptions
.Rinstignore
DESCRIPTION
NAMESPACE
NEWS
R
R/hiReadsProcessor.R
README.md
build
build/vignette.rds
data
data/FLX_seqProps.RData
data/psl.RData
inst
inst/doc
inst/doc/Tutorial.R
inst/doc/Tutorial.Rmd
inst/doc/Tutorial.html
inst/extdata
inst/extdata/FLX_sample_run
inst/extdata/FLX_sample_run/RunData
inst/extdata/FLX_sample_run/RunData/1.TCA.454Reads.fna.gz
inst/extdata/FLX_sample_run/RunData/2.TCA.454Reads.fna.gz
inst/extdata/FLX_sample_run/RunData/3.TCA.454Reads.fna.gz
inst/extdata/FLX_sample_run/Vectors
inst/extdata/FLX_sample_run/Vectors/HIV1.fa
inst/extdata/FLX_sample_run/Vectors/MLV-vector.fa
inst/extdata/FLX_sample_run/sampleInfo.xlsx
inst/tests
inst/tests/runTests.R
inst/tests/tests
inst/tests/tests/test_coreFeatures.R
man
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
vignettes
vignettes/Tutorial.Rmd
vignettes/hiReadsProcessor_object.png
vignettes/hiReadsProcessor_workflow.png
hiReadsProcessor documentation built on May 20, 2017, 9:48 p.m.

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