| aa2codons | Find the DNA to code for a given amino acid |
| aa2dna | Convert amino acids to dna regex |
| addSnpsToGenome | Add SNPs and indels to a reference sequence |
| adjustWindow | Convenience function for selecting multiple elements from a... |
| allSameLength | Convenience function to check all args are same length |
| ambiguous2regex | Converts ambiguous dna to an appropriate regular expression |
| ambiguousBaseCodes | Ambiguous base codes |
| aminoAcids | Amino acid for RNA codons |
| anyArgsNA | Convenience function to check whether any args have NAs |
| arrow | Find coords for plotting horizontal arrows |
| bases2ambiguous | Convert set of single bases to ambiguous code |
| binary2range | Find covered ranges in binary data |
| blat2exons | Take coordinates of blat matches and split into a single line... |
| blatFindGaps | Find gaps in blat coordinates |
| blatReadsVsRefs | Make a 2bit file from one set of reads and blat another set... |
| blockToAlign | Convert blocks from blat into alignment |
| cacheOperation | Cache an operation to disk or load if cache file present |
| chao | Calculate chao diversity index |
| checkBlat | Check if blat is running on port |
| chooseAtLeastOneFromEach | Calculate the number of combinations possible from nGroups... |
| cigarToBlock | Convert cigar and starts to qStarts, tStarts, blockSizes as... |
| cleanMclapply | A function to break an mclapply into parts, save to disk and... |
| codons2aa | Convert codon to amino acid |
| complementDna | Complement DNA |
| conservativeBoundary | Get the conservative edge of a confidence interval |
| convertLineToUser | Convert from axis line to user coordinates |
| convertUserToLine | Convert from user coordinates to axis line |
| countNmers | Count nMers in a string |
| cumpaste | Cumulative paste convenience function |
| cutBlatReads | Take the output from blat and make continous reads out of it |
| cv.glm.par | Check predictions of glm by cross validation |
| degap | Remove gap characters from DNA sequences |
| dna2aa | Convert dna/rna to amino acids |
| dna2codons | Convert DNA string into seperate codons |
| escapeRegexBracketChars | Convenience function to escape characters for insertion into... |
| expandAmbiguous | Convert ambiguous dna to all possible sequences |
| fillCover | Fill zeros in cover data |
| fillDown | Convenience function to fill values down a column |
| fillList | Loop through list, get unique names and make sure every... |
| fillZeros | Fill missing position with zeros |
| findIntrons | Convert set of starts and ends of exons to introns |
| flow2seq | Convert 454 flows to DNA sequences |
| gap2NoGap | Convert gapped coordinates to what the coordinates would be... |
| gcPercent | Calculate GC percentage for strings |
| generateFasta | Generate fake name and sequence data |
| gini | Calculate Gini index |
| highlightDifferences | Switch the case of positions in seq1 that mismatch seq2 |
| highlightString | Find pattern in strings and flip case |
| index2range | Find covered ranges with numerical index data |
| indexFlow | Find flow corresponding to a given base position |
| indexMatrix | Convenience function for selecting multiple elements from a... |
| insetScale | Add an inset color scale to a plot |
| intsToQual | Convert fastq chars to integer quals |
| isError | Convenience function to check for errors in a list of results... |
| jensenShannon | Calculate Jensen Shannon divergence between two probability... |
| killBlat | Kill blat running on a given port |
| kullback | Calculate Kullback-Leibler divergence between two probability... |
| lagNA | Convenience function for lagging with NA |
| liftCoords | Run liftover to convert coordinates from one genome version... |
| logAxis | Add a pretty log axis to a plot |
| mostAbundant | Convenience function for picking first most abundant of a set... |
| movingStat | Calculating a moving average/max/min statistic over a vector |
| multiBlatReadsVsRefs | Run blatReadsVsRefs in parallel |
| multiRunBlatNoServer | Run blat from parallel blat executables |
| multiYAxis | Add multiple text labels to the left axis of a plot |
| noGap2Gap | Convert ungapped coordinates to what the coordinates would be... |
| object.sizes | Convenience function to list objects by size |
| orderIn | Find the order of one vector in another |
| parseRegion | Parse a region string into chr, start, end and strand |
| pasteRegion | Make region from chr start end |
| pRare | Calculate the probability of observing observedX species from... |
| pullRegion | Pull counts from a bam file for target region |
| pwm | Generate a PWM for a set of sequences |
| pwmToSeq | Calculate sequence for PWM |
| qualToInts | Convert fastq chars to integer quals |
| rainbow.lab | Rainbow based on circle of lab color space |
| rao | Calculate Rao diversity of a vector |
| rareEquation | Calculate rarefaction using formula |
| rarefy | Calculate rarefaction using boostrapping |
| rarefyCounts | Generate rarefied counts from a vector of counts |
| read.ace | Read an ace file |
| read.bed | Read a bed file |
| read.blast | Read a tab-delimited blast file |
| read.blat | Read a blat file |
| read.fa | Read a fasta file |
| readFaDir | Read in a bunch of fasta files in a target directory |
| read.fastq | Read fastq file |
| readLargeBlat | Read a large blat file piece by piece |
| read.phd | Read a single-read Sanger phred .phd file |
| read.sam | Read a sam file |
| read.wiggle | Read a UCSC wiggle file |
| revComp | Reverse complement dna |
| reverseAmbiguous | Reverse lookup for ambiguous base codes |
| reverseString | Reverse strings |
| runBlat | Start a blat server, run blat on file and kill blat server |
| runBlatNoServer | Run blat from blat executable instead of gfserver/client |
| samFlag | Test sam flags for values |
| samFlags | SAM/BAM flags |
| samView | Call samtools view on a sam/bam file |
| scoreFromPWM | Calculate PWM scores for sequences |
| seq2flow | Convert a DNA sequence into expected 454 flows |
| seqSplit | Convenience function for splitting a bunch of sequences into... |
| shannon | Calculate Shannon diversity of a vector |
| slantAxis | Label axis with slanted labels |
| stackRegions | Stack regions into smallest number of lines (using greedy... |
| startBlat | Start a blat server |
| stopError | Generate an error |
| table2vector | Convenience function for converting 1-d table to named vector |
| toggleCase | Swap case of a string |
| trimNs | Trim ambiguous sequence from ends of reads |
| unifracMatrix | Calculate the shared branch length from a matrix of taxonomic... |
| wilsonInt | Calculate the Wilson score interval |
| withAs | Alternative with() function with explicit naming |
| write.fa | Writes sequences to a fasta file |
| write.fastq | Writes a fastq file |
