Man pages for t-arae/bstringr
A package to use a character vector as a biological strings
| align_multi | Align multiple sequences to reference |
| align_pairwise | Align bstr sequence |
| Bio2bstr | Convert sequence to Biostrings::*StringSet object |
| bstr2BioString | Convert sequence to Biostrings::*StringSet object |
| bstr2df | bstrobj <-> data.frame |
| bstr_add_obj_at | Add object attribute |
| bstr_add_seq_at | Add sequence attribute |
| bstr_count | Count the number of matches in a bstr object |
| bstr_detect | Detect the presence or absence of a pattern in a bstr object |
| bstr_extract | Extract matching patterns from a bstr object |
| bstr_locate | Locate all positions of patterns in a bstr object |
| bstr_replace | Replace matched patterns in bstr sequences by replacements |
| bstr_replace_name | Replace names of the bstring object |
| bstr_sub_true | bstr_sub_true |
| calc_GCper | Caluculate Oligo GC% |
| calc_ident | calculate % of identical residues |
| calc_ident_mat | calculate % of identical residues |
| calc_InFusion_insert_volume | Calculate the insert volume for In-Fusion reaction |
| calc_InFusion_vector_volume | Calculate the vector volume for In-Fusion reaction |
| calc_mw | calculate molecular weight |
| calc_oligoDNATm | Calculate Oligo DNA Tm |
| case | Convert case of a bstring sequence. |
| c.bstr | Combine Values into a bstr class object |
| check_validity | Detect invalid IUPAC DNA characters |
| class_bstr | Common bstr class augments |
| compare | Compare 2 residues |
| construct_bstr | Constructer of the bstr class object |
| dstr_both | Apply function to both forward and reverse-complement... |
| dstr_complement | Return complement sequences |
| dstr_extract_orfs_from_vector | Find open reading frames from Gateway system compatible... |
| dstr_iupac2regex | Convert IUPAC CODE to regular expression |
| dstr_pcr | Calculate PCR product length |
| dstr_primer_check | Primer check |
| dstr_remove_stop | Remove stop codon from DNA sequence |
| dstr_rev_comp | Return reverse complement sequences |
| dstr_translate | Translate dna -> protein |
| format_parts_length | format bstr sequence length |
| format_parts_name | format bstr name |
| format_parts_seq | format bstr sequence |
| format_row | format bstr |
| gw | TOPO reaction and LR reaction |
| is_valid_orf | Check open reading frame validity |
| length | Sequence length in the bstr sequences. |
| mf | Calculate Oligo DNA Tm |
| orfs | Find and extract all open reading frames in a dstr object |
| parse_ACCESSION_FIELD | Parse Genbank file ACCESSION FIELD |
| parse_DEFINITION_FIELD | Parse Genbank file DIFINITION FIELD |
| parse_LOCUS_FIELD | Parse Genbank file LOCUS FIELD |
| parse_ORIGIN_FIELD | Parse Genbank file ORIGIN FIELD |
| parse_VERSION_FIELD | Parse Genbank file VERSION FIELD |
| pipe | Pipe operator |
| print.bstr | print bstr class object |
| random_seq | Generate random bstr sequences of desired lengths. |
| read_fasta | Read fasta file |
| read_genbank | Read Genbank file |
| remove | Remove all matched patterns in bstr sequences |
| reverse | Reverse bstr sequence |
| show_align | show alignment |
| sort.bstr | sort bstr |
| sub | Extract and replace subsequences from a bstr sequences |
| sub_all | Extract and replace all subsequences from a bstr sequences |
| sub-.bstr | subsetting bstr class object |
| write_fasta | write fasta file |
| write_genbank | Write Genbank file |
