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

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

AuthorWolfgang Kaisers
Date of publication2014-05-24 11:28:02
MaintainerWolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
LicenseArtistic-2.0
Version0.99.35

View on R-Forge

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: Plots DNA k-mer counts from Fastqq objects.

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: Analysis of fastq and fasta files.

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...

writeSimContFastq: writeSimContFastq: Create fastq files with simulated k-mer...

writeSimFastq: writeSimFastq: Create fastq files with simulated DNA k-mer...

Functions

ascii2char Man page
cbDistMatrix Man page
cbDistMatrix,Fastqq-method Man page
cbDistMatrix-methods Man page
char2ascii Man page
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
countFastaKmers Man page
countGenomeKmers Man page
countSpliceKmers Man page
fastqKmerLocs Man page
fastqKmerSubsetLocs Man page
fastqq Man page
Fastqq-class Man page
[,Fastqq-method Man page
fileNames Man page
fileNames,Fastqq-method Man page
fileNames-methods Man page
gcContent Man page
gcContent,Fastqq-method Man page
gcContentMatrix Man page
gcContentMatrix,Fastqq-method Man page
gcContentMatrix-methods Man page
gcContent-methods Man page
getK Man page
getK,Fastqq-method Man page
getK-methods Man page
kmerCount Man page
kmerCount,Fastqq-method Man page
kmerCount-methods Man page
kMerIndex Man page
maxSeqLen Man page
maxSeqLen,Fastqq-method Man page
maxSeqLen-methods Man page
meltDownK Man page
meltDownK,Fastqq-method Man page
meltDownK-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
mergeFastqq Man page
mergeFastqq,Fastqq-method Man page
mergeFastqq-methods Man page
[-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
phred Man page
phredDist Man page
phredDist,Fastqq-method Man page
phredDist-methods Man page
phred,Fastqq-method Man page
phred-methods Man page
phredQuantiles Man page
phredQuantiles,Fastqq-method Man page
phredQuantiles-methods Man page
phredTable Man page
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<- Man page
probeLabel<-,Fastqq-method Man page
probeLabel,Fastqq-method Man page
probeLabel<--methods Man page
probeLabel-methods Man page
propPhred Man page
propPhred,Fastqq-method Man page
propPhred-methods Man page
revCountDnaKmers Man page
seqLen Man page
seqLenCount Man page
seqLenCount,Fastqq-method Man page
seqLenCount-methods Man page
seqLen,Fastqq-method Man page
seqLen-methods Man page
seqTools Man page
seqTools-package Man page
simFastqqRunTimes Man page
sim_fq Man page
trimFastq Man page
writeFai Man page
writeSimContFastq Man page
writeSimFastq Man page

Files

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

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