abundancePerSample | abundance (reads, gamme0) per sample return 1-column data... |
classification | Classify samples by taxonomic composition |
CMStatistics | Statistics to one or multipe community matrix |
ComMA-package | ComMA R documentation |
CommunityComparison | Compare community structure |
CommunityPhyloStru | Community Phylogenetic Structure from 'picante' Package |
convertType | Convert data frame columns to different type, default to... |
distance | Calculate various multivariate distance metrics |
diverrare | Rarefaction curves using Jost diversities |
enterotype | Enterotype |
EUtils | EUtils NCBI |
firstN | Return the first 'n' elements. If 'n' is greater than... |
getMethodLines | Get lines containing Java method name. The regular expression... |
getPhylorareDF | Rarefaction curve of Phylogenetic Diversity |
getPlural | Get plural by adding 's' except special plural. |
installAllPackages | Install all dependent packages. |
IOComMA | IO functions in 'ComMA' |
JostDiversity | Jost diversity from 'vegetarian' Package |
mkdir | Create folder from 'file.path' if not exist. |
mvRowsToLast | Move rows to the last rows of data frame given a column value |
normalize | normalize given vector. |
PlotPrioritisation | Plot prioritisation |
prettyNumbers | 'prettyNumbers' provide pretty numbers with comma separator... |
printXTable | Print data fram (table) as Latex format to either file or... |
RDA | Redundancy Analysis |
readCodeCoverage | Use 'readHTMLTable' to covert the report of code coverage... |
readFile | Read a file to a data frame. |
readFileLineByLine | Read File Line By Line |
readMCMCLog | Reads MCMC log files and return a data frame whose column... |
ReadsOTUsTaxa | Taxonomy analyses for multiple data sets |
richnessPerSample | richness (OTUs/species) per sample return 1-column data frame |
shannonPerSample | Shannon index (gamma1) per sample return 1-column data frame |
spatial | Great-circle distance calculations in R |
splitPath | Split a file path into folder names vector |
stringUtils | Utils to deal with strings and characters |
TaxaUtils | Utils to preprocess taxa table |
TreeUtils | Utils to manipulate or visualise phylogenetic tree |
utilsCM | Utils to preprocess community matrix |
UtilsCombine | Utils to combine data frames or matrices into the required... |
utilsSeq | Utils to manipulate sequences or OTUs |
writeTable | Write the data fram (table) to a file. |
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