| 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 sequences | writeSimContFastq |
| writeSimFastq: Create FASTQ files with simulated DNA k-mer sequences | writeSimFastq |
