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.

Author
Wolfgang Kaisers
Date of publication
2014-05-24 11:28:02
Maintainer
Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
License
Artistic-2.0
Version
0.99.35

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...

Files in this package

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