Tools based on Biostrings (alignment, classification, database)


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Documentation for package ‘BioTools’ version 0.0-1

Help Pages

addSequences Genetic Sequences
BLAST Basic Local Alignment Search Tool (BLAST)
BLAST_help Basic Local Alignment Search Tool (BLAST)
box Boxshade: Shading Multiple Aligned Sequences
boxshade Boxshade: Shading Multiple Aligned Sequences
boxshade_help Boxshade: Shading Multiple Aligned Sequences
closeGenDB Gene Sequence databases
clustal Run Multiple Sequence Alignment (clustal) on a Set of Sequences
clustal_help Run Multiple Sequence Alignment (clustal) on a Set of Sequences
createGenDB Gene Sequence databases
findAccuracy Ribosomal Database Project (RDP) Classifier for 16S rRNA
GenClass16S Manage GenClass16S objects
GenClass16S_Greengenes Manage GenClass16S objects
GenDB Gene Sequence databases
getHierarchy Classification Hierarchy for Sequences
getIDs Classification Hierarchy for Sequences
getRank Classification Hierarchy for Sequences
getSequences Genetic Sequences
getTaxonomyNames Classification Hierarchy for Sequences
GreengenesMetaDataReader Manage GenClass16S objects
kalign Multiple Sequence Alignment (kalign)
kalign_help Multiple Sequence Alignment (kalign)
listGenDB Gene Sequence databases
metaGenDB Gene Sequence databases
nSequences Genetic Sequences
openGenDB Gene Sequence databases
plot Plot Genetic Sequences and Alignments
plot.DNAMultipleAlignment Plot Genetic Sequences and Alignments
plot.DNAStringSet Plot Genetic Sequences and Alignments
plot.RNAMultipleAlignment Plot Genetic Sequences and Alignments
plot.RNAStringSet Plot Genetic Sequences and Alignments
predict Ribosomal Database Project (RDP) Classifier for 16S rRNA
predict.BLAST Basic Local Alignment Search Tool (BLAST)
predict.RDPClassifier Ribosomal Database Project (RDP) Classifier for 16S rRNA
print.BLAST Basic Local Alignment Search Tool (BLAST)
print.GenDB Gene Sequence databases
print.RDPClassifier Ribosomal Database Project (RDP) Classifier for 16S rRNA
RDP Ribosomal Database Project (RDP) Classifier for 16S rRNA
removeRDP Ribosomal Database Project (RDP) Classifier for 16S rRNA
reopenGenDB Gene Sequence databases
Sequences Genetic Sequences
simRank Compute the SimRank Similarity between Sets of Sequences
trainRDP Ribosomal Database Project (RDP) Classifier for 16S rRNA