Global functions | |
---|---|
.Modifer_to_ModifierSet | Source code |
.Modifier | Source code |
.ModifierSet | Source code |
.SequenceData | Source code |
.SequenceDataFrame | Source code |
.SequenceDataList | Source code |
.SequenceDataSet | Source code |
.add_viz_colours | Source code |
.add_viz_names | Source code |
.add_viz_ylim | Source code |
.aggregate_data_frame_mean_sd | Source code |
.aggregate_data_frame_percentage_mean_sd | Source code |
.aggregate_inosine | Source code |
.aggregate_list_data_mean_sd | Source code |
.aggregate_pile_up_to_coverage | Source code |
.all_are_existing_files | Source code |
.are_colours | Source code |
.are_whole_numbers | Source code |
.as.list.SequenceDataList | Source code |
.as.list.SequenceDataSet | Source code |
.assemble_data_per_compare_type | Source code |
.assemble_scanBamParam | Source code |
.bam_header_to_seqinfo | Source code |
.bamfiles_to_ModifierSet | Source code |
.calculate_inosine_score | Source code |
.check_Modifier_data_elements | Source code |
.check_SequenceDataList_data_elements | Source code |
.check_SequenceData_elements | Source code |
.check_aggregate_modifier | Source code |
.check_aggregate_seqdata | Source code |
.check_bamfiles | Source code |
.check_for_invalid_positions | Source code |
.check_positions_in_data | Source code |
.check_ranges | Source code |
.check_sequences | Source code |
.clean_mcols_coverage | Source code |
.clean_mcols_end | Source code |
.clean_mcols_mod_inosine | Source code |
.clean_mcols_normend | Source code |
.clean_mcols_pileup | Source code |
.compare_ModifierSet_by_GRanges | Source code |
.compare_ModifierSet_by_GRangesList | Source code |
.compare_element_metadata | Source code |
.construct_coord_from_name_from_to | Source code |
.contains_only_Modifier | Source code |
.contains_only_bamfiles | Source code |
.create_position_labels | Source code |
.create_sample_labels | Source code |
.dataTracks,ModInosine,GRanges,GRanges,XString-method | Man page |
.empty_character | Source code |
.fill_up_pileup_data | Source code |
.find_inosine | Source code |
.getData | Man page |
.get_ModDNA_bio_color | Source code |
.get_ModRNA_bio_color | Source code |
.get_SequenceData_args | Source code |
.get_bamfiles_stats | Source code |
.get_classname_for_ModifierSet_from_modifier_type | Source code |
.get_coverage_from_GA | Source code |
.get_data_for_visualization | Source code |
.get_data_stats | Source code |
.get_element_names | Source code |
.get_first_class_extends | Source code |
.get_inosine_score | Source code |
.get_modification_full_name | Source code |
.get_modifications_per_transcript | Source code |
.get_modified_sequences | Source code |
.get_name_in_parent | Source code |
.get_name_in_parent_list | Source code |
.get_position_data_of_transcript_coverage | Source code |
.get_position_data_of_transcript_ends | Source code |
.get_position_data_of_transcript_ends_norm | Source code |
.get_position_data_of_transcript_pileup | Source code |
.get_prediction_data_Modifier | Source code |
.get_prediction_data_ModifierSet | Source code |
.get_read_stats | Source code |
.get_replicate_number | Source code |
.get_strand_u_GRangesList | Source code |
.get_summary_MultiColSequenceData | Source code |
.get_summary_SequenceData | Source code |
.get_viz_annotation_track | Source code |
.get_viz_from_to | Source code |
.get_viz_from_to_coord | Source code |
.get_viz_sequence | Source code |
.get_viz_sequence_track | Source code |
.get_which_label | Source code |
.is_a_bool | Source code |
.is_a_string | Source code |
.is_function | Source code |
.is_non_empty_character | Source code |
.is_non_empty_string | Source code |
.is_not_GRanges_or_GRangesList | Source code |
.is_numeric_string | Source code |
.is_valid_DNAmodType | Source code |
.is_valid_RNAmodType | Source code |
.is_valid_modType | Source code |
.is_valid_nucleotide_seqtype | Source code |
.keep_one_labels_column | Source code |
.label_Modifier_by_GRangesList | Source code |
.label_SequenceDataList_by_GRangesList | Source code |
.label_SequenceDataSet_by_GRangesList | Source code |
.label_SequenceData_by_GRangesList | Source code |
.label_SplitDataFrameList_by_GRangesList | Source code |
.load_SequenceData | Source code |
.load_annotation | Source code |
.load_bam_alignment_data | Source code |
.load_sequences | Source code |
.merge_summary_data | Source code |
.new_ModFromCharacter | Source code |
.new_ModFromSequenceData | Source code |
.new_SequenceData | Source code |
.norm_ModInosine_settings | Source code |
.norm_ModifierSet_args | Source code |
.norm_Modifier_input_SequenceData_elements | Source code |
.norm_Modifier_settings | Source code |
.norm_aggregate_data | Source code |
.norm_alias | Source code |
.norm_annotation | Source code |
.norm_annotation_GRangesList | Source code |
.norm_bamfiles | Source code |
.norm_classname_ModifierSet | Source code |
.norm_compare_args | Source code |
.norm_compare_plot_args | Source code |
.norm_conditions | Source code |
.norm_coord | Source code |
.norm_coord_for_visualization | Source code |
.norm_data | Source code |
.norm_gff | Source code |
.norm_min_quality | Source code |
.norm_mod | Source code |
.norm_modifiertype | Source code |
.norm_performance_args | Source code |
.norm_plot_args | Source code |
.norm_postprocess_read_data | Source code |
.norm_prediction_args | Source code |
.norm_replicates | Source code |
.norm_score_type | Source code |
.norm_seqinfo | Source code |
.norm_seqnames | Source code |
.norm_sequence_data | Source code |
.norm_sequences | Source code |
.norm_settings | Source code |
.norm_show_argument | Source code |
.norm_subset_args | Source code |
.norm_unique_seqnames | Source code |
.norm_viz_args_Modifier | Source code |
.norm_viz_args_ModifierSet | Source code |
.norm_viz_args_SequenceData | Source code |
.norm_viz_chromosome | Source code |
.norm_viz_colour | Source code |
.norm_viz_colours | Source code |
.norm_viz_mod_inosine_args | Source code |
.norm_viz_pileup_args | Source code |
.norm_viz_windows.size | Source code |
.normlize_data_against_one_sample | Source code |
.not_colours | Source code |
.not_integer_bigger_equal_than_one | Source code |
.not_integer_bigger_equal_than_one_nor_na | Source code |
.not_integer_bigger_equal_than_zero | Source code |
.not_integer_bigger_equal_than_zero_nor_na | Source code |
.not_integer_bigger_than_10 | Source code |
.not_integer_bigger_than_zero | Source code |
.not_logical_operator | Source code |
.not_numeric_between_0_1 | Source code |
.not_numeric_between_0_100 | Source code |
.not_numeric_bigger_zero | Source code |
.not_single_integer | Source code |
.not_single_integer_or_na | Source code |
.not_single_numeric_or_na | Source code |
.order_read_data_by_strand | Source code |
.perform_label | Source code |
.perform_subset | Source code |
.plot_ROCR | Source code |
.plot_compare_ModifierSet | Source code |
.plot_compare_ModifierSet_by_GRanges | Source code |
.plot_compare_ModifierSet_by_GRangesList | Source code |
.process_coverage_data | Source code |
.readjust_plot_args | Source code |
.rebase_seqnames | Source code |
.seqnames_rl | Source code |
.seqs_l_by | Source code |
.seqs_partitioning | Source code |
.seqs_rl | Source code |
.seqs_rl_by | Source code |
.seqs_rl_strand | Source code |
.show_settings | Source code |
.splitPileupAsList_transcript | Source code |
.stitch_chromosome | Source code |
.strands_rl | Source code |
.subset_ModifierSet_by_GRangesList | Source code |
.subset_Modifier_by_GRangesList | Source code |
.subset_SequenceDataList_by_GRangesList | Source code |
.subset_SequenceDataSet_by_GRangesList | Source code |
.subset_SequenceData_by_GRangesList | Source code |
.subset_SplitDataFrameList_by_GRangesList | Source code |
.subset_by_seqinfo | Source code |
.subset_to_condition | Source code |
.summarize_to_position_data | Source code |
.test_setting | Source code |
.test_test_FALSE | Source code |
.test_test_TRUE | Source code |
.valid.SequenceData | Source code |
.valid.SequenceDataList | Source code |
.valid.SequenceDataList.listData | Source code |
.valid.SequenceDataSet | Source code Source code |
.valid.SequenceDataSet.listData | Source code |
.valid.SequenceData_elements | Source code |
.valid_Modifier | Source code |
.valid_ModifierSet | Source code |
.valid_SequenceData | Source code |
.valid_SequenceDataFrame | Source code |
CoverageSequenceData | Man page Source code |
CoverageSequenceData-class | Man page |
CoverageSequenceDataFrame | Man page Source code |
CoverageSequenceDataFrame-class | Man page |
DNAModifier-class | Man page |
End3SequenceData | Man page Source code |
End3SequenceData-class | Man page |
End3SequenceDataFrame | Man page Source code |
End3SequenceDataFrame-class | Man page |
End5SequenceData | Man page Source code |
End5SequenceData-class | Man page |
End5SequenceDataFrame | Man page Source code |
End5SequenceDataFrame-class | Man page |
EndSequenceData | Man page Source code |
EndSequenceData-class | Man page |
EndSequenceDataFrame | Man page Source code |
EndSequenceDataFrame-class | Man page |
ICE-Seq | Man page |
Inosine | Man page |
ModDNASequenceTrack | Man page Source code |
ModInosine | Man page Source code |
ModInosine-class | Man page |
ModInosine-functions | Man page |
ModInosine-internals | Man page |
ModRNASequenceTrack | Man page Source code |
ModSetInosine | Man page Source code |
ModSetInosine-class | Man page |
Modifier | Man page |
Modifier,BamFileList-method | Man page |
Modifier,SequenceData-method | Man page |
Modifier,SequenceDataList-method | Man page |
Modifier,SequenceDataSet-method | Man page |
Modifier,character-method | Man page |
Modifier,list-method | Man page |
Modifier-class | Man page |
Modifier-functions | Man page |
ModifierInosine | Man page |
ModifierSet | Man page |
ModifierSet,BamFileList-method | Man page |
ModifierSet,Modifier-method | Man page |
ModifierSet,character-method | Man page |
ModifierSet,list-method | Man page |
ModifierSet-class | Man page |
NormEnd3SequenceData | Man page Source code |
NormEnd3SequenceData-class | Man page |
NormEnd3SequenceDataFrame | Man page Source code |
NormEnd3SequenceDataFrame-class | Man page |
NormEnd5SequenceData | Man page Source code |
NormEnd5SequenceData-class | Man page |
NormEnd5SequenceDataFrame | Man page Source code |
NormEnd5SequenceDataFrame-class | Man page |
NormEndSequenceData-class | Man page |
PileupSequenceData | Man page Source code |
PileupSequenceData-class | Man page |
PileupSequenceDataFrame | Man page Source code |
PileupSequenceDataFrame-class | Man page |
ProtectedEndSequenceData | Man page Source code |
ProtectedEndSequenceData-class | Man page |
ProtectedEndSequenceDataFrame | Man page Source code |
ProtectedEndSequenceDataFrame-class | Man page |
RNAModifier-class | Man page |
RNAmodR | Man page |
RNAmodR-datasets | Man page |
RNAmodR-development | Man page |
RNAmodR-internals | Man page |
SequenceDFrame-class | Man page |
SequenceData | Man page |
SequenceData,GFF3File,BSgenome-method | Man page |
SequenceData,GFF3File,FaFile-method | Man page |
SequenceData,GFF3File,character-method | Man page |
SequenceData,GRangesList,BSgenome-method | Man page |
SequenceData,GRangesList,FaFile-method | Man page |
SequenceData,GRangesList,character-method | Man page |
SequenceData,TxDb,BSgenome-method | Man page |
SequenceData,TxDb,FaFile-method | Man page |
SequenceData,TxDb,character-method | Man page |
SequenceData,character,BSgenome-method | Man page |
SequenceData,character,FaFile-method | Man page |
SequenceData,character,character-method | Man page |
SequenceData-class | Man page |
SequenceData-functions | Man page |
SequenceDataFrame | Man page |
SequenceDataFrame-class | Man page |
SequenceDataList | Man page Source code |
SequenceDataList-class | Man page |
SequenceDataSet | Man page Source code |
SequenceDataSet-class | Man page |
SequenceModDNAStringSetTrack | Man page |
SequenceModDNAStringSetTrack-class | Man page |
SequenceModRNAStringSetTrack | Man page |
SequenceModRNAStringSetTrack-class | Man page |
[,SequenceDataFrame,ANY,ANY,ANY-method | Man page |
aggregate | Man page |
aggregate,Modifier-method | Man page |
aggregate,ModifierSet-method | Man page |
aggregate,SequenceData-method | Man page |
aggregate,SequenceDataList-method | Man page |
aggregate,SequenceDataSet-method | Man page |
aggregateData | Man page |
aggregateData,CoverageSequenceData-method | Man page |
aggregateData,End3SequenceData-method | Man page |
aggregateData,End5SequenceData-method | Man page |
aggregateData,EndSequenceData-method | Man page |
aggregateData,ModInosine-method | Man page |
aggregateData,Modifier-method | Man page |
aggregateData,NormEnd3SequenceData-method | Man page |
aggregateData,NormEnd5SequenceData-method | Man page |
aggregateData,PileupSequenceData-method | Man page |
aggregateData,ProtectedEndSequenceData-method | Man page |
aggregateData,SequenceData-method | Man page |
bamfiles | Man page |
bamfiles,Modifier-method | Man page |
bamfiles,ModifierSet-method | Man page |
bamfiles,SequenceData-method | Man page |
bamfiles,SequenceDataFrame-method | Man page |
bamfiles,SequenceDataList-method | Man page |
bamfiles,SequenceDataSet-method | Man page |
cbind,SequenceData-method | Man page |
cbind,SequenceDataFrame-method | Man page |
coerceSequenceDataToCompressedSplitDataFrameList | Source code |
coerceToSequenceData | Source code |
compare | Man page |
compare,ModifierSet-method | Man page |
compareByCoord | Man page |
compareByCoord,ModifierSet,GRanges-method | Man page |
compareByCoord,ModifierSet,GRangesList-method | Man page |
conditions,Modifier-method | Man page |
conditions,ModifierSet-method | Man page |
conditions,SequenceData-method | Man page |
conditions,SequenceDataFrame-method | Man page |
conditions,SequenceDataList-method | Man page |
conditions,SequenceDataSet-method | Man page |
constructModRanges | Man page |
constructModRanges,GRanges,DataFrame-method | Man page |
csd | Man page |
dataType | Man page |
dataType,Modifier-method | Man page |
dataType,ModifierSet-method | Man page |
dataType,SequenceData-method | Man page |
dataType,SequenceDataFrame-method | Man page |
e3sd | Man page |
e5sd | Man page |
esd | Man page |
findMod | Man page |
findMod,ModInosine-method | Man page |
findMod,Modifier-method | Man page |
getAggregateData | Man page |
getAggregateData,Modifier-method | Man page |
getData | Man page |
getData,CoverageSequenceData,BamFileList,GRangesList,XStringSet, | Man page |
getData,End3SequenceData,BamFileList,GRangesList,XStringSet,Scan | Man page |
getData,End5SequenceData,BamFileList,GRangesList,XStringSet,Scan | Man page |
getData,EndSequenceData,BamFileList,GRangesList,XStringSet,ScanB | Man page |
getData,NormEnd3SequenceData,BamFileList,GRangesList,XStringSet, | Man page |
getData,NormEnd5SequenceData,BamFileList,GRangesList,XStringSet, | Man page |
getData,PileupSequenceData,BamFileList,GRangesList,XStringSet,Sc | Man page |
getData,ProtectedEndSequenceData,BamFileList,GRangesList,XString | Man page |
getData,SequenceData,BamFileList,GRangesList,XStringSet,ScanBamP | Man page |
getDataTrack | Man page |
getDataTrack,CoverageSequenceData-method | Man page |
getDataTrack,End3SequenceData-method | Man page |
getDataTrack,End5SequenceData-method | Man page |
getDataTrack,EndSequenceData-method | Man page |
getDataTrack,ModInosine-method | Man page |
getDataTrack,Modifier-method | Man page |
getDataTrack,NormEnd3SequenceData-method | Man page |
getDataTrack,NormEnd5SequenceData-method | Man page |
getDataTrack,PileupSequenceData-method | Man page |
getDataTrack,ProtectedEndSequenceData-method | Man page |
getDataTrack,SequenceData-method | Man page |
getDataTrack,SequenceDataList-method | Man page |
getDataTrack,SequenceDataSet-method | Man page |
getListElement,SequenceDataList-method | Man page |
getListElement,SequenceDataSet-method | Man page |
hasAggregateData | Man page |
hasAggregateData,Modifier-method | Man page |
labelByCoord | Man page |
labelByCoord,Modifier,GRanges-method | Man page |
labelByCoord,Modifier,GRangesList-method | Man page |
labelByCoord,ModifierSet,GRanges-method | Man page |
labelByCoord,ModifierSet,GRangesList-method | Man page |
labelByCoord,SequenceData,GRanges-method | Man page |
labelByCoord,SequenceData,GRangesList-method | Man page |
labelByCoord,SequenceDataList,GRanges-method | Man page |
labelByCoord,SequenceDataList,GRangesList-method | Man page |
labelByCoord,SequenceDataSet,GRanges-method | Man page |
labelByCoord,SequenceDataSet,GRangesList-method | Man page |
labelByCoord,SplitDataFrameList,GRanges-method | Man page |
mainScore | Man page |
mainScore,Modifier-method | Man page |
mainScore,ModifierSet-method | Man page |
modType | Man page |
modType,Modifier-method | Man page |
modType,ModifierSet-method | Man page |
modifications | Man page |
modifications,Modifier-method | Man page |
modifications,ModifierSet-method | Man page |
modifierType | Man page |
modifierType,Modifier-method | Man page |
modifierType,ModifierSet-method | Man page |
modify | Man page |
modify,Modifier-method | Man page |
modify,ModifierSet-method | Man page |
msi | Man page |
names,Modifier-method | Man page |
names,SequenceDataList-method | Man page |
names,SequenceDataSet-method | Man page |
ne3sd | Man page |
ne5sd | Man page |
new_SequenceDataList_from_list | Source code |
new_SequenceDataSet_from_list | Source code |
parallel_slot_names,SequenceDataList-method | Man page |
parallel_slot_names,SequenceDataSet-method | Man page |
pesd | Man page |
pileupToCoverage | Man page |
pileupToCoverage,PileupSequenceData-method | Man page |
plotCompare | Man page |
plotCompare,ModifierSet-method | Man page |
plotCompareByCoord | Man page |
plotCompareByCoord,ModifierSet,GRanges-method | Man page |
plotCompareByCoord,ModifierSet,GRangesList-method | Man page |
plotData | Man page |
plotData,ModInosine-method | Man page |
plotData,ModSetInosine-method | Man page |
plotData,Modifier-method | Man page |
plotData,ModifierSet-method | Man page |
plotData,SequenceData-method | Man page |
plotData,SequenceDataList-method | Man page |
plotData,SequenceDataSet-method | Man page |
plotDataByCoord | Man page |
plotDataByCoord,ModInosine,GRanges-method | Man page |
plotDataByCoord,ModSetInosine,GRanges-method | Man page |
plotDataByCoord,Modifier,GRanges-method | Man page |
plotDataByCoord,ModifierSet,GRanges-method | Man page |
plotDataByCoord,SequenceData,GRanges-method | Man page |
plotDataByCoord,SequenceDataList,GRanges-method | Man page |
plotDataByCoord,SequenceDataSet,GRanges-method | Man page |
plotROC | Man page |
plotROC,Modifier-method | Man page |
plotROC,ModifierSet-method | Man page |
psd | Man page |
ranges,Modifier-method | Man page |
ranges,ModifierSet-method | Man page |
ranges,SequenceData-method | Man page |
ranges,SequenceDataFrame-method | Man page |
ranges,SequenceDataList-method | Man page |
ranges,SequenceDataSet-method | Man page |
rbind,SequenceData-method | Man page |
replicates | Man page |
replicates,Modifier-method | Man page |
replicates,ModifierSet-method | Man page |
replicates,SequenceData-method | Man page |
replicates,SequenceDataFrame-method | Man page |
replicates,SequenceDataList-method | Man page |
replicates,SequenceDataSet-method | Man page |
sdl | Man page |
sds | Man page |
seqinfo,Modifier-method | Man page |
seqinfo,ModifierSet-method | Man page |
seqinfo,SequenceData-method | Man page |
seqinfo,SequenceDataFrame-method | Man page |
seqinfo,SequenceDataList-method | Man page |
seqinfo,SequenceDataSet-method | Man page |
seqlevels,SequenceModDNAStringSetTrack-method | Man page |
seqlevels,SequenceModRNAStringSetTrack-method | Man page |
seqnames,SequenceModDNAStringSetTrack-method | Man page |
seqnames,SequenceModRNAStringSetTrack-method | Man page |
seqtype,Modifier-method | Man page |
seqtype,ModifierSet-method | Man page |
seqtype,SequenceData-method | Man page |
seqtype,SequenceDataFrame-method | Man page |
seqtype,SequenceDataList-method | Man page |
seqtype,SequenceDataSet-method | Man page |
seqtype<-,SequenceData-method | Man page |
seqtype<-,SequenceDataFrame-method | Man page |
seqtype<-,SequenceDataList-method | Man page |
seqtype<-,SequenceDataSet-method | Man page |
sequenceData | Man page |
sequenceData,Modifier-method | Man page |
sequenceDataClass | Source code |
sequenceDataFrameClass | Source code |
sequences | Man page |
sequences,Modifier-method | Man page |
sequences,ModifierSet-method | Man page |
sequences,SequenceData-method | Man page |
sequences,SequenceDataFrame-method | Man page |
sequences,SequenceDataList-method | Man page |
sequences,SequenceDataSet-method | Man page |
setSequenceDataCoercions | Source code |
settings | Man page |
settings,Modifier-method | Man page |
settings,ModifierSet-method | Man page |
settings<- | Man page |
settings<-,ModInosine-method | Man page |
settings<-,Modifier-method | Man page |
settings<-,ModifierSet-method | Man page |
show,Modifier-method | Man page |
show,ModifierSet-method | Man page |
show,SequenceData-method | Man page |
show,SequenceDataFrame-method | Man page |
show,SequenceDataList-method | Man page |
show,SequenceDataSet-method | Man page |
stats | Man page |
stats,Modifier,missing-method | Man page |
stats,ModifierSet,missing-method | Man page |
stats,SequenceData,BamFile-method | Man page |
stats,SequenceData,BamFileList-method | Man page |
subset,Modifier-method | Man page |
subset,ModifierSet-method | Man page |
subset,SequenceData-method | Man page |
subset,SequenceDataList-method | Man page |
subset,SequenceDataSet-method | Man page |
subsetByCoord | Man page |
subsetByCoord,Modifier,GRanges-method | Man page |
subsetByCoord,Modifier,GRangesList-method | Man page |
subsetByCoord,ModifierSet,GRanges-method | Man page |
subsetByCoord,ModifierSet,GRangesList-method | Man page |
subsetByCoord,SequenceData,GRanges-method | Man page |
subsetByCoord,SequenceData,GRangesList-method | Man page |
subsetByCoord,SequenceDataList,GRanges-method | Man page |
subsetByCoord,SequenceDataList,GRangesList-method | Man page |
subsetByCoord,SequenceDataSet,GRanges-method | Man page |
subsetByCoord,SequenceDataSet,GRangesList-method | Man page |
subsetByCoord,SplitDataFrameList,GRanges-method | Man page |
validAggregate | Man page |
validAggregate,Modifier-method | Man page |
validModification | Man page |
validModification,Modifier-method | Man page |
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