alexchwong/SpliceWiz
interactive analysis and visualization of alternative splicing in R

Package index
Search the alexchwong/SpliceWiz package
Vignettes
Functions
702
Source code
64
Man pages
27
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alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R
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API

API for alexchwong/SpliceWiz
interactive analysis and visualization of alternative splicing in R

Global functions
.ASE_DESeq2_contrast Source code
.ASE_DESeq2_contrast_ASE Source code
.ASE_DoubleExpSeq_contrast_ASE Source code
.ASE_add_diag Source code
.ASE_add_diag_multi Source code
.ASE_add_flags Source code
.ASE_check_args Source code
.ASE_contrast_ASE Source code
.ASE_contrast_ASE_ts Source code
.ASE_contrast_expr Source code
.ASE_contrast_expr_ts Source code
.ASE_edgeR_contrast Source code
.ASE_edgeR_contrast_ASE Source code
.ASE_edgeR_contrast_ASE_ts Source code
.ASE_edgeR_contrast_ts Source code
.ASE_edgeR_fitASE Source code
.ASE_edgeR_fitIncExc Source code
.ASE_filter Source code
.ASE_get_models Source code
.ASE_limma_contrast Source code
.ASE_limma_contrast_ASE Source code
.ASE_limma_contrast_ASE_ts Source code
.ASE_limma_contrast_ts Source code
.BAM2COV_run_single Source code
.DESeq_colData_sanitise Source code
.STAR_clean_temp_FASTA_GTF Source code
.STAR_get_FASTA Source code
.STAR_get_GTF Source code
.STAR_twopassGenome Source code
.addAnnoTrack Source code
.addBAMfiles Source code
.addCovTrack Source code
.addDiffTrack Source code
.addExonTrace Source code
.addJuncTrace Source code
.addLineTrace Source code
.addRibbonTrace Source code
.addTextTrace Source code
.adjustXrange Source code
.adjustXtitle Source code
.adjustYrange Source code
.adjustYtitle Source code
.bin_df Source code
.bin_ranges Source code
.build_GO_table Source code
.cat_ASEFilter_common Source code
.cat_ASEFilter_filterSpecific Source code
.cat_filter_info Source code
.check_2bit_performance Source code
.check_GO_species Source code
.check_cached_resource Source code
.check_ensembl Source code
.check_is_BED Source code
.check_is_BED_or_RDS Source code
.check_package_installed Source code
.collateData_COV Source code
.collateData_H5_initialize Source code
.collateData_H5_write_assays Source code
.collateData_annotate Source code
.collateData_annotate_BPPARAM Source code
.collateData_assemble_reference Source code
.collateData_cleanup Source code
.collateData_compile_agglist Source code
.collateData_compile_assays_from_fst Source code
.collateData_construct_novelGTF Source code
.collateData_expr Source code
.collateData_initialise_HDF5 Source code
.collateData_jobs Source code
.collateData_junc_annotate Source code
.collateData_junc_count Source code
.collateData_junc_group Source code
.collateData_junc_merge Source code
.collateData_junc_stats Source code
.collateData_junc_stats_merge_fn Source code
.collateData_novel_assemble_transcripts Source code
.collateData_novel_injectPutativeTJ Source code
.collateData_process_assays_as_fst Source code
.collateData_process_junc Source code
.collateData_process_splice Source code
.collateData_process_splice_depth Source code
.collateData_process_sw Source code
.collateData_rowEvent Source code
.collateData_rowEvent_brief Source code
.collateData_rowEvent_full Source code
.collateData_rowEvent_mapGenes Source code
.collateData_rowEvent_splice_option Source code
.collateData_save_NxtSE Source code
.collateData_seed_init Source code
.collateData_simplify_assay_path Source code
.collateData_simplify_assay_paths Source code
.collateData_splice_anno Source code
.collateData_stats Source code
.collateData_stats_QC Source code
.collateData_stats_reads Source code
.collateData_stop_sw_mismatch Source code
.collateData_sw_group Source code
.collateData_sw_merge Source code
.collateData_tj_annotate Source code
.collateData_tj_merge Source code
.collateData_validate Source code
.collateData_write_colData Source code
.collateData_write_stats Source code
.colourise Source code
.convert_BED_or_RDS_to_GRanges Source code
.convert_chromosomes Source code
.coord_single_range_expand_nodash Source code
.coord_single_range_expand_withdash Source code
.copy_DT Source code
.covPlotlyMake Source code
.cov_process_regions Source code
.cov_ui_inline Source code
.dash_get_memmode Source code
.dash_get_openmp Source code
.dash_get_threads Source code
.fetch_AH Source code
.fetch_AH_cache_loc Source code
.fetch_GOterms Source code
.fetch_fasta Source code
.fetch_fasta_ah Source code
.fetch_fasta_file Source code
.fetch_fasta_save_2bit Source code
.fetch_fasta_save_fasta Source code
.fetch_genome_as_required Source code
.fetch_genome_defaults Source code
.fetch_gtf Source code
.fetch_orgDB Source code
.fetch_orgDB_cache Source code
.findOverlaps_merge Source code
.findOverlaps_merge_DT Source code
.fixYrange Source code
.fix_gtf Source code
.fix_gtf_check_metadata_columns Source code
.fix_gtf_check_one_seqname_per_gene_id Source code
.fix_gtf_check_one_seqname_per_transcript_id Source code
.fix_gtf_check_type_exon Source code
.fix_gtf_fix_gene_metadata Source code
.fix_gtf_fix_transcript_metadata Source code
.fix_gtf_fix_type_gene Source code
.fix_gtf_fix_type_transcript Source code
.format_GO_result Source code
.gCD_determine_limits Source code
.gCD_determine_loci Source code
.gCD_retrieve_annotations Source code
.gCD_retrieve_colData Source code
.gCD_retrieve_junc Source code
.gCD_retrieve_norms Source code
.gCD_retrieve_raw_cov Source code
.gCD_retrieve_raw_cov_helper Source code
.gCD_validate_args Source code
.gCD_validate_args_coords Source code
.gCD_validate_args_event Source code
.gCD_validate_args_loci Source code
.gCD_validate_args_se Source code
.gPO_PSIjuncStats Source code
.gPO_check_strand Source code
.gPO_check_tracks Source code
.gPO_covStats Source code
.gPO_getCoverage Source code
.gPO_getJunc Source code
.gPO_normJuncStats Source code
.gcd_stack_anno Source code
.gen_irf Source code
.gen_irf_ROI Source code
.gen_irf_convert_seqnames Source code
.gen_irf_exclusion_zones Source code
.gen_irf_export_introncover Source code
.gen_irf_final Source code
.gen_irf_irfname Source code
.gen_irf_prep_data Source code
.gen_irf_prep_introns Source code
.gen_irf_prep_introns_unique Source code
.gen_irf_readcons Source code
.gen_irf_refcover Source code
.gen_irf_sj Source code
.gen_irf_tj Source code
.gen_nmd Source code
.gen_nmd_determine Source code
.gen_nmd_determine_build_introns_upstream Source code
.gen_nmd_determine_new Source code
.gen_nmd_determine_retrieve_full_seq Source code
.gen_nmd_determine_retrieve_short_seq Source code
.gen_nmd_determine_spliced_exon Source code
.gen_nmd_determine_translate Source code
.gen_nmd_exons_trimmed Source code
.gen_nmd_protein_introns Source code
.gen_splice Source code
.gen_splice_MXE Source code
.gen_splice_skipcoord Source code
.gencode_correct_id_batch Source code
.gencode_correct_id_indiv Source code
.generate_ggplot_GO Source code
.generate_plot_GO_labels Source code
.getGeneList Source code
.getNMDcode Source code
.getOntologySpecies Source code
.getSWthreads Source code
.get_SpliceWiz_cache Source code
.get_cache_file_path Source code
.get_discrete_cats Source code
.get_geneGO Source code
.get_reference_data Source code
.get_unified_volcano_data Source code
.get_volcano_data_FCunits Source code
.get_volcano_data_sigunits Source code
.gmr_check_params Source code
.gpo_filter_anno Source code
.gpo_highlight_anno Source code
.grDT Source code
.grlGaps Source code
.gtf_get_genome_style Source code
.infobox_update_se Source code
.injectPlotData Source code
.internal_get_coverage_as_df Source code
.is_AH_pattern Source code
.knitPlotly Source code
.loadIREvents Source code
.loadOntology Source code
.loadSpliceEvents Source code
.loadTranscripts Source code
.loadViewRef Source code
.load_NxtSE_sweetalert_error Source code
.load_NxtSE_sweetalert_finish Source code
.log Source code
.makeSE_adjust_paths Source code
.makeSE_colData_clean Source code
.makeSE_expand_assay_path Source code
.makeSE_iterate_IR Source code
.makeSE_iterate_IR_new Source code
.makeSE_iterate_IR_retrieve_excluded_introns Source code
.makeSE_iterate_IR_select_events Source code
.makeSE_iterate_IR_select_events_fast Source code
.makeSE_load_NxtSE Source code
.makeSE_progress_rowMeans Source code
.makeSE_sweetalert_error Source code
.makeSE_sweetalert_finish Source code
.makeSE_validate_args Source code
.make_path_relative Source code
.nxtcat Source code
.onAttach Source code
.ora_internal Source code
.overlaps_exon_island Source code
.pV_assemble_covPlotly2 Source code
.pV_assemble_ggplot Source code
.pV_diffStat_ttest Source code
.pV_filterTranscripts Source code
.pV_getAllowedCoords Source code
.pV_getEventCoords Source code
.pV_getJuncCoords Source code
.pV_highlight_to_colors Source code
.pV_mod_ggplot Source code
.pV_plotCoverageTracks Source code
.pV_plotDiffTracks Source code
.pV_plotExons Source code
.pV_plotRef Source code
.pV_sashimiArc Source code
.pV_seed_ggplot_HLexons Source code
.pV_seed_ggplot_annoTrack Source code
.pV_seed_ggplot_covTrack Source code
.pV_seed_ggplot_diffTrack Source code
.pV_seed_instant_plotly_HLexons Source code
.pV_seed_instant_plotly_annoTrack Source code
.pV_seed_plotly_HLexons Source code
.pV_seed_plotly_annoTrack Source code
.pV_seed_plotly_covTrack Source code
.pV_seed_plotly_diffTrack Source code
.pV_trackList_from_list Source code
.pV_trackList_from_vector Source code
.parse_valid_file Source code
.plotly_makeJuncCurveData Source code
.plotly_makeLineData Source code
.plotly_makeRectData Source code
.prepare_covplot_data Source code
.processBAM_fcfile_validate Source code
.processBAM_getStrand Source code
.processBAM_run_featureCounts Source code
.processBAM_run_single Source code
.processBAM_validate_args Source code
.process_exon_groups Source code
.process_gtf Source code
.process_gtf_exons Source code
.process_gtf_genes Source code
.process_gtf_misc Source code
.process_gtf_transcripts Source code
.process_introns Source code
.process_introns_annotate Source code
.process_introns_annotate_basics Source code
.process_introns_annotate_others Source code
.process_introns_annotate_splice_motifs Source code
.process_introns_data Source code
.process_introns_group Source code
.process_introns_group_fix_RI Source code
.process_introns_group_overlap Source code
.process_ontology Source code
.refresh_genome Source code
.refresh_gtf Source code
.refresh_releases Source code
.refresh_species Source code
.restore_threads Source code
.runFilter_anno_mode Source code
.runFilter_anno_mxe Source code
.runFilter_anno_mxe_gr_casette Source code
.runFilter_anno_nmd Source code
.runFilter_anno_pc Source code
.runFilter_anno_ssdiff Source code
.runFilter_anno_strictSS Source code
.runFilter_anno_terminus Source code
.runFilter_anno_tsl Source code
.runFilter_cond_vec Source code
.runFilter_data_consistency Source code
.runFilter_data_consistency_truths Source code
.runFilter_data_coverage Source code
.runFilter_data_depth Source code
.run_BAM2COV Source code
.run_processBAM Source code
.run_processBAM_GenerateMapReads Source code
.run_processBAM_MapExclusionRegions Source code
.save_NxtSE_sweetalert_error Source code
.save_NxtSE_sweetalert_finish Source code
.save_NxtSE_sweetalert_nonidentical Source code
.se_to_nxtse Source code
.semi_join_DT Source code
.server_cov2_getNewIRanges Source code
.server_cov2_update_events_list Source code
.server_expr_check_savestate Source code
.server_expr_gen_HOT Source code
.server_expr_load_alert_fail Source code
.server_expr_load_alert_success Source code
.server_expr_parse_collate_path Source code
.server_expr_parse_collate_path_full Source code
.server_expr_parse_collate_path_limited Source code
.server_expr_ref_load_fail Source code
.server_expr_ref_load_success Source code
.server_expr_save_expr Source code
.server_expr_simple_unify_df Source code
.server_expr_simple_unify_new_df Source code
.server_expr_sync_df Source code
.split_vector Source code
.sw_dash_get_mappa Source code
.translate_fuzzy Source code
.ui_notice Source code
.update_fields_DE Source code
.valid.NxtSE Source code
.valid.NxtSE.meta_QC Source code
.valid.NxtSE.meta_cov Source code
.valid.NxtSE.meta_exc Source code
.valid.NxtSE.meta_inc Source code
.valid.NxtSE.metadata Source code
.validate_GO_ref Source code
.validate_OTF_STAR_reference Source code
.validate_STAR_fastq_samples Source code
.validate_STAR_reference Source code
.validate_STAR_trim_sequence Source code
.validate_STAR_version Source code
.validate_genome_type Source code
.validate_gtf_chromosomes Source code
.validate_path Source code
.validate_reference Source code
.validate_reference_resource Source code
.validate_threads Source code
ASE-GLM-edgeR Man page
ASE-methods Man page
ASEFilter Man page Source code
ASEFilter-class Man page
ASE_DESeq Man page Source code
ASE_DoubleExpSeq Man page Source code
ASE_edgeR Man page Source code
ASE_edgeR_timeseries Man page Source code
ASE_limma Man page Source code
ASE_limma_timeseries Man page Source code
BAM2COV Man page Source code
Build-Reference-methods Man page
Coverage Man page
Expr_Load_Anno Source code
Expr_Load_SW Source code
Expr_PB_actually_run Source code
Expr_PB_initiate_run Source code
Expr_Update_colData Source code
Expr_cD_actually_run Source code
Expr_cD_initiate_run Source code
Expr_collateData_Validate_Vars Source code
Filters_Plot_Summary Source code
GUI Man page
Gene-ontology-methods Man page
Get_GTF_file Source code
Get_Genome Source code
Graphics-User-Interface Man page
Has_OpenMP Source code
Mappability-methods Man page
NxtSE Man page Source code
NxtSE-class Man page
NxtSE-methods Man page
QC_Bar_X Source code
QC_Bar_Y Source code
QC_PCA Source code
QC_Scatter_XY Source code
QC_update_plot Source code
Run_SpliceWiz_Filters Man page
SE_charbound Source code
STAR-methods Man page
STAR_alignExperiment Man page Source code
STAR_alignReads Man page Source code
STAR_buildGenome Man page Source code
STAR_buildRef Man page Source code
STAR_loadGenomeGTF Man page Source code
STAR_mappability Man page Source code
STAR_version Man page Source code
SpliceWiz Man page
SpliceWiz-package Man page
SpliceWizMain Source code
SpliceWizMain_multi Source code
SpliceWiz_example_NxtSE Man page Source code
SpliceWiz_example_bams Man page Source code
Test_OpenMP_For Source code
View-Reference-methods Man page
[,NxtSE,ANY,ANY,ANY-method Man page
[<-,NxtSE,ANY,ANY,NxtSE-method Man page
addPSI_edgeR Man page Source code
applyFilters Man page Source code
assay_withDimnames Source code
buildFullRef Man page Source code
buildRef Man page Source code
c_BAM2COV Source code
c_Check_Cov Source code
c_Cov_Seqnames Source code
c_GenerateMappabilityReads Source code
c_GenerateMappabilityRegions Source code
c_RLEList_From_Cov Source code
c_RLE_From_Cov Source code
c_doStats Source code
c_gunzip Source code
c_gunzip_DF Source code
calculateMappability Man page Source code
cbind,NxtSE-method Man page
coerce,SummarizedExperiment,NxtSE-method Man page
collateData Man page Source code
condition Man page
condition,covPlotObject-method Man page
coord2GR Man page Source code
covDataObject Source code
covDataObject-class Man page
covPlotObject Source code
covPlotObject-class Man page
covPlotly Source code
covPlotly-class Man page
covfile Man page
covfile,NxtSE-method Man page
covfile<- Man page
covfile<-,NxtSE-method Man page
dash_progress Source code
dash_server Source code
down_exc Man page
down_exc,NxtSE-method Man page
down_exc<- Man page
down_exc<-,NxtSE-method Man page
down_inc Man page
down_inc,NxtSE-method Man page
down_inc<- Man page
down_inc<-,NxtSE-method Man page
example-SpliceWiz-data Man page
extract_gene_ids_for_GO Man page Source code
filterModule_UI Source code
filterModule_server Source code
findBAMS Man page Source code
findFASTQ Man page Source code
findSamples Man page Source code
findSpliceWizOutput Man page Source code
fitASE_edgeR Man page Source code
fitASE_edgeR_custom Man page Source code
generateSyntheticReads Man page Source code
getAvailableGO Man page Source code
getCoverage Man page Source code
getCoverageBins Man page Source code
getCoverageData Man page Source code
getCoverageRegions Man page Source code
getCoverage_DF Man page Source code
getDefaultFilters Man page Source code
getExonRanges Man page
getExonRanges,covPlotly-method Man page
getGenomeData Man page Source code
getNonPolyARef Man page Source code
getPlotObject Man page Source code
getResources Man page Source code
get_multi_DT_from_gz Source code
goASE Man page Source code
goGenes Man page Source code
is.nan.data.frame Source code
isCOV Man page Source code
is_valid Source code
junc_PSI Man page
junc_PSI,NxtSE-method Man page
junc_counts Man page
junc_counts,NxtSE-method Man page
junc_counts_uns Man page
junc_counts_uns,NxtSE-method Man page
junc_gr Man page
junc_gr,NxtSE-method Man page
makeMatrix Man page Source code
makeMeanPSI Man page Source code
makeSE Man page Source code
make_plot_data Man page
plotAnnoTrack Man page Source code
plotCoverage Man page Source code
plotGO Man page Source code
plotGenome Man page Source code
plotView Man page Source code
processBAM Man page Source code
rbind,NxtSE-method Man page
realize_NxtSE Man page
realize_NxtSE,NxtSE-method Man page
ref Man page
ref,NxtSE-method Man page
row_gr Man page
row_gr,NxtSE-method Man page
runFilter Man page Source code
run_Gunzip Source code
sampleQC Man page
sampleQC,NxtSE-method Man page
sampleQC<- Man page
sampleQC<-,NxtSE-method Man page
sampleQC_withDimnames Source code
server_DE Source code
server_GO Source code
server_cov2 Source code
server_expr Source code
server_filters Source code
server_qc Source code
server_ref_new Source code
server_vis_diag Source code
server_vis_heatmap Source code
server_vis_volcano Source code
setResolution Man page
setResolution,covPlotly-method Man page
setSWthreads Man page Source code
set_dimnames Source code
setreactive_Cov Source code
setreactive_Cov2 Source code
setreactive_DE Source code
setreactive_Diag Source code
setreactive_GO Source code
setreactive_Heat Source code
setreactive_QC Source code
setreactive_expr Source code
setreactive_filtered_SE Source code
setreactive_newref Source code
setreactive_system Source code
shinyDirAttnButton Source code
shinyFilesAttnButton Source code
shinySaveAttnButton Source code
showEvents Man page
showEvents,covDataObject-method Man page
showExons Man page
showExons,covPlotly-method Man page
simplify_NULL_dimnames Source code
sourcePath Man page
sourcePath,NxtSE-method Man page
spliceWiz Man page Source code
subset_EventNames_by_GO Man page Source code
testASE_edgeR Man page Source code
theme_white Man page
theme_white_legend Man page
theme_white_legend_plot_track Man page
tracks Man page
tracks,covPlotObject-method Man page
ui_DE Source code
ui_GO Source code
ui_cov_new Source code
ui_ddb_anno Source code
ui_ddb_anno_io Source code
ui_ddb_build_annos Source code
ui_ddb_demo_load Source code
ui_ddb_exprSettings Source code
ui_ddb_find_expr_folder Source code
ui_ddb_load_expr Source code
ui_ddb_novel_splicing_settings Source code
ui_ddb_project_dir Source code
ui_ddb_ref_load Source code
ui_ddb_save_NxtSE Source code
ui_ddb_sw_path Source code
ui_ddb_sys Source code
ui_expr Source code
ui_expr_limited Source code
ui_filters Source code
ui_infobox_bam Source code
ui_infobox_expr Source code
ui_infobox_pb Source code
ui_infobox_ref Source code
ui_qc Source code
ui_ref_new Source code
ui_sidebar Source code
ui_tab_GO Source code
ui_tab_analyse Source code
ui_tab_coverage Source code
ui_tab_diag Source code
ui_tab_expr Source code
ui_tab_expr_load Source code
ui_tab_filter Source code
ui_tab_heatmap Source code
ui_tab_qc Source code
ui_tab_ref_new Source code
ui_tab_title Source code
ui_tab_volcano Source code
ui_toggle_wellPanel Source code
ui_toggle_wellPanel_modular Source code
ui_vis_diag Source code
ui_vis_heatmap Source code
ui_vis_volcano Source code
ui_wellPanel_anno Source code
up_exc Man page
up_exc,NxtSE-method Man page
up_exc<- Man page
up_exc<-,NxtSE-method Man page
up_inc Man page
up_inc,NxtSE-method Man page
up_inc<- Man page
up_inc<-,NxtSE-method Man page
update_NxtSE Man page
update_NxtSE,NxtSE-method Man page
update_data_frame Source code
vector_withDimnames Source code
viewASE Man page Source code
viewExons Man page Source code
viewGO Man page Source code
viewGenes Man page Source code
viewIR Man page Source code
viewIR_NMD Man page Source code
viewIntrons Man page Source code
viewProteins Man page Source code
viewTranscripts Man page Source code
visFilter_UI Source code
visFilter_server Source code
vis_ggplot_UI Source code
vis_ggplot_server Source code
alexchwong/SpliceWiz documentation built on April 17, 2025, 5:15 p.m.

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