Man pages for seqTools
Analysis of nucleotide, sequence and quality content on fastq files

ascii2charascii2char: Converting ASCII encoded values to character...
cbDistMatrixcbDistMatrix function: Calculates pairwise distance matrix...
collectDurcollectDur: Returning elapsed time (in seconds) for...
countDnaKmerscountDnaKmers: Counting k-mers in DNA sequence.
countFastaKmerscountFastaKmers function: Counts DNA k-mers from (compressed)...
countGenomeKmerscountGenomeKmers: Counting K-mers in DNA sequences.
countSpliceKmerscountSpliceKmers: Counting K-mers on donor (5', upstream)...
fastqKmerLocsfastqKmerLocs function: Counts DNA k-mers position wise from...
fastqKmerSubsetLocsfastqKmerSubsetLocs function: Counts for a given DNA k-mer...
fastqqfastqq function: Reading summarizing information from FASTQ...
Fastqq-classClass '"Fastqq"'
gcContentMatrixgcContentMatrix: Returns matrix with read counts for GC...
kMerIndexkMerIndex function: Returns array index for given DNA k-mers.
meltDownKmeltDownK: Condensing DNA k-mer count data to lower k-value...
mergedPhredmergedPhred functions: Retrieving and plotting of phred...
mergeFastqqmergeFastqq: Merges two Fastqq object into one.
phredDistphredDist: Global relative content of Phred values in Fastqq...
phredTablephredTable: Returns a data.frame with phred encodings.
plotGCcontentplotGCcontent: Plots the proportions of relative GC content...
plotKmerCountplotKmerCount: Creation of plots DNA for k-mer counts from...
plotNucCountplotNucCount: Plots nucleotide counts from Fastqq objects.
plotNucFreqplotNucFreq: Plots the position wise relative nucleotide...
plotPhredQuantplotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75%...
propPhredpropPhred: Lane specific proportion of reads in a specified...
revCountDnaKmersrevCountDnaKmers: Counting K-mers in DNA sequence.
seqTools-packageSeqTools: Bioconductor package for analysis of FASTQ and...
simFastqqRunTimessimFastqqRunTimes: For given values of k and nSeq the...
sim_fqsim_fq: Performs an experimental series of separation...
trimFastqtrimFastq: Performs sequence removal, trimming (fixed and...
writeFaiwriteFai: Create FASTA index file.
writeSimContFastqwriteSimContFastq: Create FASTQ files with simulated k-mer...
writeSimFastqwriteSimFastq: Create FASTQ files with simulated DNA k-mer...
seqTools documentation built on Nov. 17, 2017, 2:09 p.m.