| 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... |
