RNAmodR
Detection of post-transcriptional modifications in high throughput sequencing data

Package index
Search the RNAmodR package
Vignettes
Functions
562
Source code
47
Man pages
30
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RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data
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API

API for RNAmodR
Detection of post-transcriptional modifications in high throughput sequencing data

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
RNAmodR documentation built on Dec. 15, 2020, 2 a.m.

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