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

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>
Date of publicationNone
MaintainerNirav V Malani <malnirav@gmail.com>
LicenseGPL-3
Version1.10.0

View on Bioconductor

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

Files

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

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