Man pages for hallucigenia-sparsa/seqgroup
Analysis of Sequencing Data with Groups

aggregateTaxaAggregate a taxon abundance matrix
assignColorsToGroupsAssign colors to groups
assignMetadataTypesAssign data types to metadata
barebonesCoNetBarebones R implementation of CoNet
buildNetworkBuild a microbial network
clrCentered log-ratio (CLR) transform
compareDistribsCompare the distribution of a taxon across two groups
compareGroupsCompare diversity-related properties across groups
exportToCoNetExport taxon abundances in a format suitable for CoNet
filterMetadataFilter metadata
filterTaxonMatrixFilter taxa in an abundance matrix
findClustersCluster taxon- or sample-wise
getCoreTaxaList core taxa across groups
groupBarplotBar plot of taxon composition with group support
ibd_functionsFunctions from the PRISM cohort
ibd_lineagesLineages for taxa from the PRISM cohort
ibd_metadataMetadata for the PRISM cohort
ibd_taxaIBD and control taxon abundances from the PRISM cohort
intersectTablesTable intersection
mergeATCMerge ATC codes
mergeTablesTable union
metadataToNumericConvert metadata into numeric form
networkIntersectSigSignificance of network intersection
normalizeNormalize a matrix
selectSamplesGivenMetadataSplit samples into groups given metadata.
seqgroupAnalysis of Sequencing Data with Groups
seqPCoAPCoA for microbial sequencing data
setNAToGroupMeanReplace missing values by group mean.
silhouetteGet silhouette score for cluster labels
toPhyloseqConvert abundances to phyloseq object
transitionProbabsCompute transition probabilities between clusters
hallucigenia-sparsa/seqgroup documentation built on June 15, 2020, 10:37 p.m.