Function reference • CompGenomicsBioc2022

Loading Genome Data

Functions for loading and visualizing genomic data

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)

Gene Calling and Annotation

Functions for calling and annotating genetic regions

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)

Constructing COGs

Functions to construct COGs from annotated genetic regions

DisjointSet(): Return single linkage clusters from PairSummaries objects. (from SynExtend)

ExtractBy(): Extract and organize DNAStringSetss. (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)

Constructing Phylogenies

Functions for phylogenetic reconstruction of genomes or COGs

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)

Finding Co-evolving Gene Collectives

Functions for finding co-evolutionary signal between COGs

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)