Man pages for t-arae/bstringr
A package to use a character vector as a biological strings

align_multiAlign multiple sequences to reference
align_pairwiseAlign bstr sequence
Bio2bstrConvert sequence to Biostrings::*StringSet object
bstr2BioStringConvert sequence to Biostrings::*StringSet object
bstr2dfbstrobj <-> data.frame
bstr_add_obj_atAdd object attribute
bstr_add_seq_atAdd sequence attribute
bstr_countCount the number of matches in a bstr object
bstr_detectDetect the presence or absence of a pattern in a bstr object
bstr_extractExtract matching patterns from a bstr object
bstr_locateLocate all positions of patterns in a bstr object
bstr_replaceReplace matched patterns in bstr sequences by replacements
bstr_replace_nameReplace names of the bstring object
calc_GCperCaluculate Oligo GC%
calc_identcalculate % of identical residues
calc_ident_matcalculate % of identical residues
calc_InFusion_insert_volumeCalculate the insert volume for In-Fusion reaction
calc_InFusion_vector_volumeCalculate the vector volume for In-Fusion reaction
calc_mwcalculate molecular weight
calc_oligoDNATmCalculate Oligo DNA Tm
caseConvert case of a bstring sequence.
c.bstrCombine Values into a bstr class object
check_validityDetect invalid IUPAC DNA characters
class_bstrCommon bstr class augments
compareCompare 2 residues
construct_bstrConstructer of the bstr class object
dstr_bothApply function to both forward and reverse-complement...
dstr_complementReturn complement sequences
dstr_extract_orfs_from_vectorFind open reading frames from Gateway system compatible...
dstr_iupac2regexConvert IUPAC CODE to regular expression
dstr_pcrCalculate PCR product length
dstr_primer_checkPrimer check
dstr_remove_stopRemove stop codon from DNA sequence
dstr_rev_compReturn reverse complement sequences
dstr_translateTranslate dna -> protein
format_parts_lengthformat bstr sequence length
format_parts_nameformat bstr name
format_parts_seqformat bstr sequence
format_rowformat bstr
gwTOPO reaction and LR reaction
is_valid_orfCheck open reading frame validity
lengthSequence length in the bstr sequences.
mfCalculate Oligo DNA Tm
orfsFind and extract all open reading frames in a dstr object
parse_LOCUS_FIELDParse Genbank file LOCUS FIELD
parse_ORIGIN_FIELDParse Genbank file ORIGIN FIELD
pipePipe operator
print.bstrprint bstr class object
random_seqGenerate random bstr sequences of desired lengths.
read_fastaRead fasta file
read_genbankRead Genbank file
removeRemove all matched patterns in bstr sequences
reverseReverse bstr sequence
show_alignshow alignment
sort.bstrsort bstr
subExtract and replace subsequences from a bstr sequences
sub_allExtract and replace all subsequences from a bstr sequences
sub-.bstrsubsetting bstr class object
write_fastawrite fasta file
write_genbankWrite Genbank file
t-arae/bstringr documentation built on March 18, 2021, 3:08 a.m.