seqTools: Analysis of nucleotide, sequence and quality content on fastq files
Version 1.10.0

Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files.

Browse man pages Browse package API and functions Browse package files

AuthorWolfgang Kaisers
Bioconductor views QualityControl Sequencing
Date of publicationNone
MaintainerWolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
LicenseArtistic-2.0
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("seqTools")

Man pages

ascii2char: ascii2char: Converting ASCII encoded values to character...
cbDistMatrix: cbDistMatrix function: Calculates pairwise distance matrix...
collectDur: collectDur: Returning elapsed time (in seconds) for...
countDnaKmers: countDnaKmers: Counting k-mers in DNA sequence.
countFastaKmers: countFastaKmers function: Counts DNA k-mers from (compressed)...
countGenomeKmers: countGenomeKmers: Counting K-mers in DNA sequences.
countSpliceKmers: countSpliceKmers: Counting K-mers on donor (5', upstream)...
fastqKmerLocs: fastqKmerLocs function: Counts DNA k-mers position wise from...
fastqKmerSubsetLocs: fastqKmerSubsetLocs function: Counts for a given DNA k-mer...
fastqq: fastqq function: Reading summarizing information from FASTQ...
Fastqq-class: Class '"Fastqq"'
gcContentMatrix: gcContentMatrix: Returns matrix with read counts for GC...
kMerIndex: kMerIndex function: Returns array index for given DNA k-mers.
meltDownK: meltDownK: Condensing DNA k-mer count data to lower k-value...
mergedPhred: mergedPhred functions: Retrieving and plotting of phred...
mergeFastqq: mergeFastqq: Merges two Fastqq object into one.
phredDist: phredDist: Global relative content of Phred values in Fastqq...
phredTable: phredTable: Returns a data.frame with phred encodings.
plotGCcontent: plotGCcontent: Plots the proportions of relative GC content...
plotKmerCount: plotKmerCount: Creation of plots DNA for k-mer counts from...
plotNucCount: plotNucCount: Plots nucleotide counts from Fastqq objects.
plotNucFreq: plotNucFreq: Plots the position wise relative nucleotide...
plotPhredQuant: plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75%...
propPhred: propPhred: Lane specific proportion of reads in a specified...
revCountDnaKmers: revCountDnaKmers: Counting K-mers in DNA sequence.
seqTools-package: SeqTools: Bioconductor package for analysis of FASTQ and...
simFastqqRunTimes: simFastqqRunTimes: For given values of k and nSeq the...
sim_fq: sim_fq: Performs an experimental series of separation...
trimFastq: trimFastq: Performs sequence removal, trimming (fixed and...
writeFai: writeFai: Create FASTA index file.
writeSimContFastq: writeSimContFastq: Create FASTQ files with simulated k-mer...
writeSimFastq: writeSimFastq: Create FASTQ files with simulated DNA k-mer...

Functions

Fastqq-class Man page
[,Fastqq-method Man page
[-methods Man page
ascii2char Man page Source code
cbDistMatrix Man page
cbDistMatrix,Fastqq-method Man page
cbDistMatrix-methods Man page
char2ascii Man page Source code
collectDur Man page
collectDur,Fastqq-method Man page
collectDur-methods Man page
collectTime Man page
collectTime,Fastqq-method Man page
collectTime-methods Man page
countDnaKmers Man page Source code
countFastaKmers Man page Source code
countGenomeKmers Man page Source code
countSpliceKmers Man page Source code
enlargeIntMat Source code
fastqKmerLocs Man page Source code
fastqKmerSubsetLocs Man page Source code
fastqq Man page Source code
fileNames Man page
fileNames,Fastqq-method Man page
fileNames-methods Man page
gcContent Man page
gcContent,Fastqq-method Man page
gcContent-methods Man page
gcContentMatrix Man page
gcContentMatrix,Fastqq-method Man page
gcContentMatrix-methods Man page
getGCcontent Man page
getGCcontent,Fastqq-method Man page
getGCcontent-methods Man page
getK Man page
getK,Fastqq-method Man page
getK-methods Man page
kMerIndex Man page Source code
kmerCount Man page
kmerCount,Fastqq-method Man page
kmerCount-methods Man page
listMelt Source code
maxSeqLen Man page
maxSeqLen,Fastqq-method Man page
maxSeqLen-methods Man page
meltDownK Man page
meltDownK,Fastqq-method Man page
meltDownK-methods Man page
mergeFastqq Man page
mergeFastqq,Fastqq-method Man page
mergeFastqq-methods Man page
mergedPhred Man page
mergedPhred,Fastqq-method Man page
mergedPhred-methods Man page
mergedPhredQuantiles Man page
mergedPhredQuantiles,Fastqq-method Man page
mergedPhredQuantiles-methods Man page
nFiles Man page
nFiles,Fastqq-method Man page
nFiles-methods Man page
nNnucs Man page
nNnucs,Fastqq-method Man page
nNnucs-methods Man page
nReads Man page
nReads,Fastqq-method Man page
nReads-methods Man page
nucFreq Man page
nucFreq,Fastqq-method Man page
nucFreq-methods Man page
onUnload Source code Source code
pd_l10 Source code
phred Man page
phred,Fastqq-method Man page
phred-methods Man page
phredDist Man page
phredDist,Fastqq-method Man page
phredDist-methods Man page
phredQuantiles Man page
phredQuantiles,Fastqq-method Man page
phredQuantiles-methods Man page
phredTable Man page Source code
plotGCcontent Man page
plotGCcontent,Fastqq-method Man page
plotGCcontent-methods Man page
plotKmerCount Man page
plotKmerCount,Fastqq-method Man page
plotKmerCount-methods Man page
plotMergedPhredQuant Man page
plotMergedPhredQuant,Fastqq-method Man page
plotMergedPhredQuant-methods Man page
plotNucCount Man page
plotNucCount,Fastqq-method Man page
plotNucCount-methods Man page
plotNucFreq Man page
plotNucFreq,Fastqq-method Man page
plotNucFreq-methods Man page
plotPhredDist Man page
plotPhredDist,Fastqq-method Man page
plotPhredDist-methods Man page
plotPhredQuant Man page
plotPhredQuant,Fastqq-method Man page
plotPhredQuant-methods Man page
probeLabel Man page
probeLabel,Fastqq-method Man page
probeLabel-methods Man page
probeLabel<- Man page
probeLabel<-,Fastqq-method Man page
probeLabel<--methods Man page
propPhred Man page
propPhred,Fastqq-method Man page
propPhred-methods Man page
rel_int Source code
rel_real Source code
revCountDnaKmers Man page Source code
seqLen Man page
seqLen,Fastqq-method Man page
seqLen-methods Man page
seqLenCount Man page
seqLenCount,Fastqq-method Man page
seqLenCount-methods Man page
seqTools Man page
seqTools-package Man page
simFastqqRunTimes Man page Source code
sim_fq Man page Source code
trimFastq Man page Source code
writeFai Man page Source code
writeSimContFastq Man page Source code
writeSimFastq Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/allClasses.R
R/allGenerics.R
R/allStatics.R
R/fastaFunctions.R
R/kMer.R
R/seqTools.R
R/simFunctions.R
R/trimFastq.R
build
build/vignette.rds
inst
inst/doc
inst/doc/seqTools.R
inst/doc/seqTools.Rnw
inst/doc/seqTools.pdf
inst/doc/seqTools_qual_report.R
inst/doc/seqTools_qual_report.Rnw
inst/doc/seqTools_qual_report.pdf
inst/extdata
inst/extdata/g4_l101_n100.fq.gz
inst/extdata/g5_l101_n100.fq.gz
inst/extdata/sfq1_cont.fq.gz
inst/extdata/sfq1_ctrl.fq.gz
inst/extdata/sfq2_cont.fq.gz
inst/extdata/sfq2_ctrl.fq.gz
inst/extdata/sim.fq.gz
inst/extdata/small.fa
inst/extdata/small.fa.gz
inst/extdata/test_buftest.fq
inst/extdata/test_l10_20_40.fq
inst/extdata/test_l10_ATCGN.fq
inst/extdata/test_l10_atcg.fq
inst/extdata/test_l4.fq
inst/extdata/test_l5_N.fq
inst/extdata/test_l6.fq
inst/extdata/test_l6_LF_end.fq
inst/extdata/test_l6_corrupt.fq
inst/extdata/test_l6_multi_line.fq
inst/extdata/test_res.RData
man
man/Fastqq-class.Rd
man/ascii2char.Rd
man/cbDistMatrix.Rd
man/collectDur.Rd
man/countDnaKmers.Rd
man/countFastaKmers.Rd
man/countGenomeKmers.Rd
man/countSpliceKmers.Rd
man/fastqKmerLocs.Rd
man/fastqKmerSubsetLocs.Rd
man/fastqq.Rd
man/gcContentMatrix.Rd
man/kMerIndex.Rd
man/meltDownK.Rd
man/mergeFastqq.Rd
man/mergedPhred.Rd
man/phredDist.Rd
man/phredTable.Rd
man/plotGCcontent.Rd
man/plotKmerCount.Rd
man/plotNucCount.Rd
man/plotNucFreq.Rd
man/plotPhredQuant.Rd
man/propPhred.Rd
man/revCountDnaKmers.Rd
man/seqTools-package.Rd
man/simFastqqRunTimes.Rd
man/sim_fq.Rd
man/trimFastq.Rd
man/writeFai.Rd
man/writeSimContFastq.Rd
man/writeSimFastq.Rd
src
src/Makevars
src/Makevars.win
src/dna_astream.h
src/dna_fasta_stream.h
src/dna_fstream.h
src/fa_traverse.h
src/fastq_parser.h
src/fq_traverse.h
src/resize_matrix.h
src/seqTools.c
src/seqTools.h
src/seq_art.h
src/stat_defs.h
tests
tests/test-all.R
tests/test_seqTools.r
vignettes
vignettes/seqTools.Rnw
vignettes/seqTools.bib
vignettes/seqTools_qual_report.Rnw
seqTools documentation built on May 20, 2017, 9:36 p.m.