Fastqq-class            Class '"Fastqq"'
ascii2char              ascii2char: Converting ASCII encoded values to
                        character values.
cbDistMatrix            cbDistMatrix function: Calculates pairwise
                        distance matrix from DNA k-mer counts based on
                        a modified Canberra distance.
collectDur              collectDur: Returning elapsed time (in seconds)
                        for collection of data from FASTQ files.
countDnaKmers           countDnaKmers: Counting k-mers in DNA sequence.
countFastaKmers         countFastaKmers function: Counts DNA k-mers
                        from (compressed) fasta files.
countGenomeKmers        countGenomeKmers: Counting K-mers in DNA
                        sequences.
countSpliceKmers        countSpliceKmers: Counting K-mers on donor (5',
                        upstream) sides (exonic) of splice sites.
fastqKmerLocs           fastqKmerLocs function: Counts DNA k-mers
                        position wise from FASTQ files.
fastqKmerSubsetLocs     fastqKmerSubsetLocs function: Counts for a
                        given DNA k-mer subset position wise from FASTQ
                        files.
fastqq                  fastqq function: Reading summarizing
                        information from FASTQ files.
gcContentMatrix         gcContentMatrix: Returns matrix with read
                        counts for GC content.
kMerIndex               kMerIndex function: Returns array index for
                        given DNA k-mers.
meltDownK               meltDownK: Condensing DNA k-mer count data to
                        lower k-value (i.e. shorter DNA motifs).
mergeFastqq             mergeFastqq: Merges two Fastqq object into one.
mergedPhred             mergedPhred functions: Retrieving and plotting
                        of phred quantities from whole 'Fastqq'
                        objects.
phredDist               phredDist: Global relative content of Phred
                        values in Fastqq objects (or subsets).
phredTable              phredTable: Returns a data.frame with phred
                        encodings.
plotGCcontent           plotGCcontent: Plots the proportions of
                        relative GC content for all FASTQ files.
plotKmerCount           plotKmerCount: Creation of plots DNA for k-mer
                        counts from Fastqq objects.
plotNucCount            plotNucCount: Plots nucleotide counts from
                        Fastqq objects.
plotNucFreq             plotNucFreq: Plots the position wise relative
                        nucleotide content for nucleotides
                        'A','C','G','T'.
plotPhredQuant          plotPhredQuant: Plots the position wise 10%, 25
                        %, 50%, 75% and 90 % quantiles of phred values.
propPhred               propPhred: Lane specific proportion of reads in
                        a specified Phred-region.
revCountDnaKmers        revCountDnaKmers: Counting K-mers in DNA
                        sequence.
seqTools-package        SeqTools: Bioconductor package for analysis of
                        FASTQ and fasta files.
simFastqqRunTimes       simFastqqRunTimes: For given values of k and
                        nSeq the function creates FASTQ files with
                        simulated data, collects k-mer data with the
                        fastqq function and reports the run times for
                        the data collection.
sim_fq                  sim_fq: Performs an experimental series of
                        separation capabilities of hierarchical
                        clustering (HC) based on DNA k-mers in FASTQ
                        files using simulated DNA content.
trimFastq               trimFastq: Performs sequence removal, trimming
                        (fixed and quality based) and nucleotide
                        masking on FASTQ files.
writeFai                writeFai: Create FASTA index file.
writeSimContFastq       writeSimContFastq: Create FASTQ files with
                        simulated k-mer sequences
writeSimFastq           writeSimFastq: Create FASTQ files with
                        simulated DNA k-mer sequences
