addGenomes | Add new organisms to an existing pangenome |
addGroupInfo | Safely add group info |
addOrgInfo | Safely add organisms info |
cdhitGrouping | Gene grouping by preclustering with CD-HIT |
collapseParalogues | Merge paralogue gene groups into new gene groups |
defaults | Access default values for a pgVirtual subclass object |
fillDefaults | Assign object defaults to missing values |
FindMyFriends-package | FindMyFriends: Comparative microbial genomics in R |
geneLocation | Get gene location for all genes |
geneNames | Get and set the names of the genes in the pangenome |
genes | Extract gene sequences from a pangenome |
geneWidth | Get the sequence length of each gene |
getNeighborhood | Extract a graph representation of a gene group neighborhood |
getRep | Get a representative sequence for each gene group |
gpcGrouping | Guided Pairwise Comparison grouping of genes |
graphGrouping | Use igraph to create gene grouping from a similarity matrix |
groupInfo | Get and set information about gene group |
groupNames | Get and set the names of gene groups in the pangenome |
groupStat | Calculate statistics about each gene group |
hasGeneGroups | Check whether gene groups are defined |
hasGeneInfo | Checks for existance of gene location information |
hasParalogueLinks | Checks whether linking of paralogues has been done |
internalGroupGenes | Add gene grouping to pangenome |
internalMergePangenomes | Merge information from two pangenomes |
internalMetadata | Add metadata to the pangenome |
kmerLink | Link gene groups by homology |
kmerSimilarity | Calculate a similarity matrix based on kmers |
kmerSplit | Split gene groups based on similarity |
loadPgExample | Load an example pangenome |
manualGrouping | Define gene grouping manually |
neighborhoodSplit | Split gene groups by neighborhood synteny |
nGeneGroups | Get the number of gene groups in a pangenome |
nGenes | Get the total number of genes in a pangenome |
nOrganisms | Get the number of organisms represented in a pangenome |
orgInfo | Get and set information about organisms |
orgNames | Get and set the names of organisms in the pangenome |
orgStat | Calculate statistics about each organism |
pangenome | Construct a pangenome from fasta files |
pcGraph | Calculate the panchromosome graph |
pgFull-class | Class for in memory pangenome data |
pgFullLoc-class | Class for in memory pangenome data with location information |
pgInMem-class | FindMyFriends standard base class for pangenomic data |
pgInMemLoc-class | Superclass for gene location aware pangenome |
pgLM-class | Class for reference based pangenome data |
pgLMLoc-class | Class for reference based pangenome data with location... |
pgMatrix | Get the pangenome matrix |
pgSlim-class | Class for pangenome data with no reference to genes |
pgSlimLoc-class | Class for pangenome data with no reference to genes |
pgVirtual-class | Base class for pangenomic data |
pgVirtualLoc-class | Superclass for gene location aware pangenome |
plotEvolution | Plot the evolution in gene groups |
plotGroup | Plot the similarities of genes within a group |
plotNeighborhood | Plot the neighborhood of a gene group |
plotSimilarity | Create a heatplot with similarities between all organisms |
plotStat | Plot (very) basic statistics on the pangenome |
plotTree | Plot a dendrogram of the organisms in a pangenome |
readAnnot | Import annotation from an .annot file |
removeGene | Remove genes from a pangenome |
reportGroupChanges | Reports the change in grouping |
seqToGeneGroup | Get gene-to-genegroup relationship |
seqToOrg | Get gene-to-organism relationship |
translated | Check the sequence type of the pangenome |
variableRegions | Detect regions of high variability in the panchromosome |
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