Man pages for michbur/tidysq
Tidy processing and analysis of biological sequences

AAindexAmino acids properties
aminoacids_dfAmino acid abbreviations
as.character.sqConvert sq object into character vector
as.matrix.sqConvert sq object into matrix
as.sqConvert an object to sq
bg_freqsAmino Acid Residue Background Frequencies
biteSubset sequences from sq objects
BLOSUM50The BLOSUM50 matrix
BLOSUM50_encThe BLOSUM50_enc matrix
BLOSUM50_pcaThe BLOSUM50_pca matrix
BLOSUM62The BLOSUM62 matrix
BLOSUM62_encThe BLOSUM62_enc matrix
BLOSUM62_pcaThe BLOSUM62_pca matrix
cleanClean sequences containing ambiguous elements
complementCreate complement sequence from dnasq or rnasq object
construct_sqConstruct sq object from character vector
digestDigest proteins at specified cleavage sites
encodeEncode sequences as numeric values
encsq_to_listTransform encoded sequence to a list
equals-.sqCompare sq objects
export_sqExport sq objects into other formats
fast-modeMake your operations faster
find_motifsFind given motifs
get_invalid_lettersFind elements which are not suitable for specified type.
get_sq_alphabetGet alphabet of given sq object.
get_sq_lengthsGet lengths of sequences in sq object
get_sq_typeGet type of a sq object
get_tidysq_optionsObtain current state of tidysq options
grapes-has-grapesTest sq object for presence of given motifs
import_sqImport sq objects from other objects
is_null_sqTest if a sequence is empty
is.sqCheck if object has specified type
nucleotides_dfNucleotides abbreviations
random_sqGenerate random sequences
read_fastaRead a FASTA file
remove_naRemove sequences containing NA values
reverseReverse sequence
sqsq: class for keeping biological sequences tidy
sqapplyApply function to each sequence
sqconcatenateConcatenate sq objects
sqextractExtract parts of a sq object
sqprintPrint sq object
substitute_lettersSubstitute letters in a sequence
tidysq-optionsSet options of package
tidysq-packagetidysq: tidy analysis of biological sequences
typifySet type of untyped and atypical sequences
write_fastaSave sq to fasta file
michbur/tidysq documentation built on Sept. 17, 2020, 5:16 a.m.