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 standalone BLAT.
blatSeqs                Align sequences using BLAT.
chunkize                Breaks an object into chunks of N size.
clusterSites            Cluster/Correct values within a window based on
                        their frequency given discrete factors
crossOverCheck          Remove values/positions which are overlapping
                        between discrete groups based on their
                        frequency.
dereplicateReads        Removes duplicate sequences from DNAStringSet
                        object.
doRCtest                Test if pattern aligns better in +/-
                        orientation.
extractFeature          Extract a specific feature/attribute of the
                        sampleInfo object.
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 object.
findLTRs                Find the 5' LTRs and add results to SampleInfo
                        object.
findLinkers             Find the 3' linkers 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 object.
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 a population
hiReadsProcessor        Functions to process LM-PCR reads from
                        454/Illumina data.
isuSites                Bin values or make ISUs by assigning a unique
                        ID to them within discrete factors.
otuSites                Bin values or make OTUs by assigning a unique
                        ID to them within discrete factors.
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 sequences.
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.SeqFolder          Read contents of a sequencing folder and make a
                        SimpleList object
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 metadata.
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 identifier or vector
sampleSummary           Simple summary of a sampleInfo object.
seqProps                Sample Integration Sites Sequencing Data
splitByBarcode          Split DNAStringSet object using first X number
                        of bases defined by a vector.
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
