Function reference
-
BrowseSeqs()
- View Sequences in a Web Browser (from DECIPHER)
-
FindSynteny()
- Finds Synteny in a Sequence Database (from DECIPHER)
-
pairs(<Synteny>)
plot(<Synteny>)
print(<Synteny>)
- Synteny blocks and hits (from DECIPHER)
-
AlignSeqs()
- Align a Set of Unaligned Sequences (from DECIPHER)
-
AlignTranslation()
- Align Sequences By Their Amino Acid Translation (from DECIPHER)
-
AlignSynteny()
- Pairwise Aligns Syntenic Blocks (from DECIPHER)
-
BrowseDB()
- View a Database Table in a Web Browser (from DECIPHER)
-
SearchDB()
- Obtain Specific Sequences from a Database (from DECIPHER)
-
Seqs2DB()
- Add Sequences from Text File to Database (from DECIPHER)
-
DB2Seqs()
- Export Database Sequences to a FASTA or FASTQ File (from DECIPHER)
-
FindGenes()
- Find Genes in a Genome (from DECIPHER)
-
FindNonCoding()
- Find Non-Coding RNAs in a Genome (from DECIPHER)
-
LearnNonCoding()
- Learn a Non-Coding RNA Model (from DECIPHER)
-
IdTaxa()
- Assign Sequences a Taxonomic Classification (from DECIPHER)
-
plot(<Taxa>)
print(<Taxa>)
`[`(<Taxa>)
- Taxa training and testing objects (from DECIPHER)
-
LearnTaxa()
- Train a Classifier for Assigning Taxonomy (from DECIPHER)
-
DisjointSet()
- Return single linkage clusters from
PairSummaries
objects. (from SynExtend)
-
ExtractBy()
- Extract and organize
DNAStringSets
s. (from SynExtend)
-
FindSets()
- Find all single linkage clusters in an undirected pairs list. (from SynExtend)
-
print(<LinkedPairs>)
- Tables of where syntenic hits link pairs of genes (from SynExtend)
-
NucleotideOverlap()
- Tabulating Pairs of Genomic Sequences (from SynExtend)
-
PairSummaries()
- Summarize connected pairs in a LinkedPairs object (from SynExtend)
-
BlockExpansion()
- Attempt to expand blocks of paired features in a
PairSummaries
object. (from SynExtend)
-
Cophenetic()
- Compute cophenetic distances on dendrogram objects (from DECIPHER)
-
DistanceMatrix()
- Calculate the Distances Between Sequences (from DECIPHER)
-
Clusterize()
- Cluster Sequences By Distance (from DECIPHER)
-
TreeLine()
- Construct a Phylogenetic Tree (from DECIPHER)
-
WriteDendrogram()
- Write a Dendrogram to Newick Format (from DECIPHER)
-
ProtWeaver()
SpeciesTree(<ProtWeaver>)
- ProtWeaver: Predicting Protein Functional Association Networks (from SynExtend)
-
predict(<ProtWeaver>)
- Make predictions with ProtWeaver objects (from SynExtend)
-
simMat()
as.simMat(<vector>)
as.simMat(<matrix>)
print(<simMat>)
as.matrix(<simMat>)
as.data.frame(<simMat>)
Diag(<simMat>)
`Diag<-`(<simMat>)
- Similarity Matrices (from SynExtend)
- ProtWeb: Predictions from ProtWeaver (from SynExtend)
-
plot(<ProtWeb>)
- Plot predictions in a ProtWeb object (from SynExtend)