API for FelixErnst/Modstrings
Working with modified nucleotide sequences

Global functions
.ModDNAorRNAcodes Source code
.ModStringSet.alphabet_frequency Source code
.ModStringSet.alphabet_frequency_Set Source code
.ModStringSet.show_frame Source code
.ModStringSet.show_frame_line Source code
.add_lower_to_upper_case Source code
.add_moddna_colors Source code
.add_modrna_colors Source code
.add_modx_colors Source code
.call_XString_replace_letter_at Source code
.call_fasta_index Source code
.call_new_CHARACTER_from_XStringSet Source code
.check_fastq_markup Source code
.check_for_invalid_letters Source code
.check_letter_ModStringSet Source code
.check_replace_pos_ModStringSet Source code
.check_stop.on.error Source code
.check_verbose Source code
.combine_modifications Source code
.combine_modifications_in_GRanges Source code
.combine_modifications_in_GRangesList Source code
.combine_to_new_nc_ident Source code
.compare_ModString Source code
.compare_ModStringSet Source code
.compare_ModString_Views Source code
.construct_translation_table Source code
.convert_letters_to_one_byte_codes Source code
.convert_letters_to_originating_base Source code
.convert_one_byte_codes_to_letters Source code
.convert_one_byte_codes_to_originating_base Source code
.convert_to_QualityScaledStringSet Source code
.detect_seqtype_in_GRanges Source code
.detect_seqtype_in_GRangesList Source code
.escape_special_charactes Source code
.fasta.index Source code
.format_as_fasta Source code
.format_as_fastq Source code
.format_utf8 Source code
.from_ModStringSet_to_GRanges Source code
.get_XStringQuality_from_GRanges Source code
.get_names_from_fastq_block Source code
.get_nc_ident Source code
.get_nc_type Source code
.get_sequences_from_fastq_block Source code
.get_short_nc_lib Source code
.incompatbile_modifications Source code
.load_mod_dictionary Source code
.merge_non_unique_mcols Source code
.merge_non_unique_mcols_do Source code
.new_ModStringCodec Source code
.norm_GRanges Source code
.norm_GRangesList Source code
.norm_GRangesList_for_combine Source code
.norm_GRangesList_for_separate Source code
.norm_GRanges_for_combine Source code
.norm_GRanges_for_separate Source code
.norm_replace_pos_ModString Source code
.norm_seqtype_modtype Source code
.onLoad Source code
.parse_fasta_block Source code
.pos_to_logical_list Source code
.pos_to_logical_matrix Source code
.read_ModStringSet Source code
.read_ModStringSet_from_fasta_file_data Source code
.read_ModStringSet_from_fasta_index Source code
.read_ModStringSet_from_fastq Source code
.read_ModStringSet_from_fastq_file_data Source code
.read_ModStringSet_from_ssorted_fasta_index Source code
.separate_modifications Source code
.separate_modifications_in_GRanges Source code
.separate_modifications_in_GRangesList Source code
.str_replace_all_fixed_custom Source code
.str_replace_all_regex_custom Source code
.write_ModStringSet_to_fasta Source code
.write_ModStringSet_to_fastq Source code
==,ModString,ModString-method Man page
==,ModString,XString-method Man page
==,ModStringSet,ModStringSet-method Man page
==,ModStringSet,XStringSet-method Man page
==,ModStringViews,ModStringViews-method Man page
==,ModStringViews,XString-method Man page
==,XString,ModString-method Man page
==,XStringSet,ModStringSet-method Man page
==,XStringViews,ModString-method Man page
MOD_RNA_DICT_MODOMICS Man page
MOD_RNA_DICT_TRNADB Man page
MaskedModString Man page
ModDNAString Man page Source code
ModDNAString-class Man page
ModDNAStringSet Man page Source code
ModDNAStringSet-class Man page
ModDNAStringSetList Man page Source code
ModDNAStringSetList-class Man page
ModRNAString Man page Source code
ModRNAString-class Man page
ModRNAStringSet Man page Source code
ModRNAStringSet-class Man page
ModRNAStringSetList Man page Source code
ModRNAStringSetList-class Man page
ModString Man page
ModString,AsIs-method Man page
ModString,MaskedModString-method Man page
ModString,ModString-method Man page
ModString,XString-method Man page
ModString,character-method Man page
ModString,factor-method Man page
ModStringSet Man page
ModStringSet,ANY-method Man page
ModStringSet,AsIs-method Man page
ModStringSet,ModString-method Man page
ModStringSet,ModStringSet-method Man page
ModStringSet,ModStringViews-method Man page
ModStringSet,character-method Man page
ModStringSet,factor-method Man page
ModStringSet,list-method Man page
ModStringSet,missing-method Man page
ModStringSet-io Man page
ModStringSetList Man page
ModStringViews Man page
Modstrings Man page
Modstrings-internals Man page
QualityScaledModDNAStringSet Man page Source code
QualityScaledModDNAStringSet-class Man page
QualityScaledModRNAStringSet Man page Source code
QualityScaledModRNAStringSet-class Man page
QualityScaledModStringSet Man page
Views,ModString-method Man page
XString,ModString-method Man page
XStringSet,ModStringSet-method Man page
add_colors Source code
alphabet Man page
alphabet,ModString-method Man page
alphabet,ModStringSet-method Man page
alphabetFrequency Man page
alphabetFrequency,MaskedModString-method Man page
alphabetFrequency,ModDNAString-method Man page
alphabetFrequency,ModDNAStringSet-method Man page
alphabetFrequency,ModRNAString-method Man page
alphabetFrequency,ModRNAStringSet-method Man page
as.character,ModString-method Man page
as.character,ModStringSet-method Man page
as.vector,ModString-method Man page
combineIntoModstrings Man page
combineIntoModstrings,XString,GRanges-method Man page
combineIntoModstrings,XStringSet,GRanges-method Man page
combineIntoModstrings,XStringSet,GRangesList-method Man page
combineModifications Man page
combineModifications,GRanges-method Man page
combineModifications,GRangesList-method Man page
comparable_seqtypes Source code
consensusMatrix,ModStringSet-method Man page
consensusString Man page
consensusString,ModDNAStringSet-method Man page
consensusString,ModRNAStringSet-method Man page
consensusString,ModStringViews-method Man page
fullName Man page
fullName,ModString-method Man page
fullName,ModStringSet-method Man page
hasOnlyBaseLetters Man page
hasOnlyBaseLetters,ModDNAString-method Man page
hasOnlyBaseLetters,ModDNAStringSet-method Man page
hasOnlyBaseLetters,ModRNAString-method Man page
hasOnlyBaseLetters,ModRNAStringSet-method Man page
incompatibleModifications Man page
incompatibleModifications,GRanges,XString-method Man page
incompatibleModifications,GRanges,XStringSet-method Man page
incompatibleModifications,GRangesList,XStringSet-method Man page
letterFrequency Man page
letterFrequency,MaskedModString-method Man page
letterFrequency,ModStringViews-method Man page
letterFrequencyInSlidingView Man page
make_MODDNA_COLORED_LETTERS Source code
make_MODRNA_COLORED_LETTERS Source code
modifyNucleotides Man page
modifyNucleotides,DNAString-method Man page
modifyNucleotides,DNAStringSet-method Man page
modifyNucleotides,ModString-method Man page
modifyNucleotides,ModStringSet-method Man page
modifyNucleotides,RNAString-method Man page
modifyNucleotides,RNAStringSet-method Man page
modsDNA Man page
modsRNA Man page
modscodec Source code
modsnomenclature Source code
modsshortnames Source code
nomenclature Man page
nomenclature,ModString-method Man page
nomenclature,ModStringSet-method Man page
readModDNAStringSet Man page Source code
readModRNAStringSet Man page Source code
readQualityScaledModDNAStringSet Man page Source code
readQualityScaledModRNAStringSet Man page Source code
removeIncompatibleModifications Man page
removeIncompatibleModifications,GRanges,XString-method Man page
removeIncompatibleModifications,GRanges,XStringSet-method Man page
removeIncompatibleModifications,GRangesList,XStringSet-method Man page
replaceLetterAt Man page
replaceLetterAt,ModString-method Man page
replaceLetterAt,ModStringSet-method Man page
sanitizeFromModomics Man page Source code
sanitizeFromtRNAdb Man page Source code
sanitizeInput Man page Source code
separate Man page
separate,GRanges-method Man page
separate,GRangesList-method Man page
separate,ModString-method Man page
separate,ModStringSet-method Man page
seqtype,MaskedModString-method Man page
seqtype,ModDNAString-method Man page
seqtype,ModRNAString-method Man page
seqtype<-,ModString-method Man page
seqtype<-,ModStringSet-method Man page
shortName Man page
shortName,ModString-method Man page
shortName,ModStringSet-method Man page
show,ModStringSet-method Man page
show,ModStringViews-method Man page
show,QualityScaledModStringSet-method Man page
writeModStringSet Man page Source code
writeQualityScaledModStringSet Man page Source code
FelixErnst/Modstrings documentation built on March 21, 2020, 11:38 p.m.