Package: seqTools 1.41.0

Wolfgang Kaisers

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.

Authors:Wolfgang Kaisers

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seqTools/json (API)
NEWS

# Install 'seqTools' in R:
install.packages('seqTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • zlib– Compression library

On BioConductor:seqTools-1.41.0(bioc 3.21)seqTools-1.40.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

qualitycontrolsequencingzlib

5.57 score 1 packages 52 scripts 275 downloads 6 mentions 52 exports 1 dependencies

Last updated 2 months agofrom:a203e7839e. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 14 2024
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R-4.5-linux-x86_64WARNINGDec 14 2024
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R-4.4-mac-x86_64WARNINGDec 14 2024
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Exports:ascii2charcbDistMatrixchar2asciicollectDurcollectTimecountDnaKmerscountFastaKmerscountGenomeKmerscountSpliceKmersfastqKmerLocsfastqKmerSubsetLocsfastqqfileNamesgcContentgcContentMatrixgetGCcontentgetKkmerCountkMerIndexkmerSvdmaxSeqLenmeltDownKmergedPhredmergedPhredQuantilesmergeFastqqnFilesnNnucsnReadsnucFreqphredphredDistphredQuantilesphredTableplotGCcontentplotKmerCountplotMergedPhredQuantplotNucCountplotNucFreqplotPhredDistplotPhredQuantprobeLabelprobeLabel<-propPhredrevCountDnaKmersseqLenseqLenCountsim_fqsimFastqqRunTimestrimFastqwriteFaiwriteSimContFastqwriteSimFastq

Dependencies:zlibbioc

Introduction

Rendered fromseqTools.Rnwusingutils::Sweaveon Dec 14 2024.

Last update: 2014-10-13
Started: 2014-10-13

seqTools_qual_report

Rendered fromseqTools_qual_report.Rnwusingutils::Sweaveon Dec 14 2024.

Last update: 2015-12-22
Started: 2014-10-13

Readme and manuals

Help Manual

Help pageTopics
SeqTools: Bioconductor package for analysis of FASTQ and fasta files.seqTools-package seqTools
ascii2char: Converting ASCII encoded values to character values.ascii2char char2ascii
cbDistMatrix function: Calculates pairwise distance matrix from DNA k-mer counts based on a modified Canberra distance.cbDistMatrix cbDistMatrix,Fastqq-method cbDistMatrix-methods
collectDur: Returning elapsed time (in seconds) for collection of data from FASTQ files.collectDur collectDur,Fastqq-method collectDur-methods collectTime collectTime,Fastqq-method collectTime-methods
countDnaKmers: Counting k-mers in DNA sequence.countDnaKmers
countFastaKmers function: Counts DNA k-mers from (compressed) fasta files.countFastaKmers
countGenomeKmers: Counting K-mers in DNA sequences.countGenomeKmers
countSpliceKmers: Counting K-mers on donor (5', upstream) sides (exonic) of splice sites.countSpliceKmers
fastqKmerLocs function: Counts DNA k-mers position wise from FASTQ files.fastqKmerLocs
fastqKmerSubsetLocs function: Counts for a given DNA k-mer subset position wise from FASTQ files.fastqKmerSubsetLocs
fastqq function: Reading summarizing information from FASTQ files.fastqq
Class '"Fastqq"'Fastqq-class fileNames fileNames,Fastqq-method fileNames-methods gcContent gcContent,Fastqq-method gcContent-methods getK getK,Fastqq-method getK-methods kmerCount kmerCount,Fastqq-method kmerCount-methods maxSeqLen maxSeqLen,Fastqq-method maxSeqLen-methods nFiles nFiles,Fastqq-method nFiles-methods nNnucs nNnucs,Fastqq-method nNnucs-methods nReads nReads,Fastqq-method nReads-methods nucFreq nucFreq,Fastqq-method nucFreq-methods phred phred,Fastqq-method phred-methods phredQuantiles phredQuantiles,Fastqq-method phredQuantiles-methods probeLabel probeLabel,Fastqq-method probeLabel-methods probeLabel<- probeLabel<-,Fastqq-method probeLabel<--methods seqLen seqLen,Fastqq-method seqLen-methods seqLenCount seqLenCount,Fastqq-method seqLenCount-methods [,Fastqq-method [-methods
gcContentMatrix: Returns matrix with read counts for GC content.gcContentMatrix gcContentMatrix,Fastqq-method gcContentMatrix-methods getGCcontent getGCcontent,Fastqq-method getGCcontent-methods
kMerIndex function: Returns array index for given DNA k-mers.kMerIndex
meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs).meltDownK meltDownK,Fastqq-method meltDownK-methods
mergedPhred functions: Retrieving and plotting of phred quantities from whole 'Fastqq' objects.mergedPhred mergedPhred,Fastqq-method mergedPhred-methods mergedPhredQuantiles mergedPhredQuantiles,Fastqq-method mergedPhredQuantiles-methods plotMergedPhredQuant plotMergedPhredQuant,Fastqq-method plotMergedPhredQuant-methods
mergeFastqq: Merges two Fastqq object into one.mergeFastqq mergeFastqq,Fastqq-method mergeFastqq-methods
phredDist: Global relative content of Phred values in Fastqq objects (or subsets).phredDist phredDist,Fastqq-method phredDist-methods plotPhredDist plotPhredDist,Fastqq-method plotPhredDist-methods
phredTable: Returns a data.frame with phred encodings.phredTable
plotGCcontent: Plots the proportions of relative GC content for all FASTQ files.plotGCcontent plotGCcontent,Fastqq-method plotGCcontent-methods
plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects.plotKmerCount plotKmerCount,Fastqq-method plotKmerCount-methods
plotNucCount: Plots nucleotide counts from Fastqq objects.plotNucCount plotNucCount,Fastqq-method plotNucCount-methods
plotNucFreq: Plots the position wise relative nucleotide content for nucleotides 'A','C','G','T'.plotNucFreq plotNucFreq,Fastqq-method plotNucFreq-methods
plotPhredQuant: Plots the position wise 10%, 25 %, 50%, 75% and 90 % quantiles of phred values.plotPhredQuant plotPhredQuant,Fastqq-method plotPhredQuant-methods
propPhred: Lane specific proportion of reads in a specified Phred-region.propPhred propPhred,Fastqq-method propPhred-methods
revCountDnaKmers: Counting K-mers in DNA sequence.revCountDnaKmers
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.sim_fq
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.simFastqqRunTimes
trimFastq: Performs sequence removal, trimming (fixed and quality based) and nucleotide masking on FASTQ files.trimFastq
writeFai: Create FASTA index file.writeFai
writeSimContFastq: Create FASTQ files with simulated k-mer sequenceswriteSimContFastq
writeSimFastq: Create FASTQ files with simulated DNA k-mer sequenceswriteSimFastq