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 |
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