alexchwong/NxtIRFcore
Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

Package index
Search the alexchwong/NxtIRFcore package
Vignettes
Functions
327
Source code
27
Man pages
19
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alexchwong/NxtIRFcore: Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine
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API

API for alexchwong/NxtIRFcore
Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

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_check_args Source code
.ASE_filter Source code
.ASE_limma_contrast Source code
.ASE_limma_contrast_ASE Source code
.BAM2COV_run_single Source code
.DESeq_colData_sanitise Source code
.MakeSE_load_NxtSE Source code
.STAR_clean_temp_FASTA_GTF Source code
.STAR_get_FASTA Source code
.STAR_get_GTF Source code
.bin_gr Source code
.cat_NxtFilter_common Source code
.cat_NxtFilter_filterSpecific Source code
.cat_filter_info Source code
.check_is_BED 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_compile_agglist Source code
.collateData_compile_assays_from_fst Source code
.collateData_expand_assay_path Source code
.collateData_expand_assay_paths Source code
.collateData_expr Source code
.collateData_initialise_HDF5 Source code
.collateData_irf_group Source code
.collateData_irf_merge Source code
.collateData_jobs Source code
.collateData_junc_annotate Source code
.collateData_junc_group Source code
.collateData_junc_merge Source code
.collateData_process_assays_as_fst Source code
.collateData_process_irf Source code
.collateData_process_junc Source code
.collateData_process_splice Source code
.collateData_process_splice_depth Source code
.collateData_rowEvent Source code
.collateData_rowEvent_brief Source code
.collateData_rowEvent_full 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_irf_mismatch Source code
.collateData_validate Source code
.collateData_write_colData Source code
.collateData_write_stats Source code
.colourise Source code
.convert_chromosomes Source code
.coord_single_range_expand_nodash Source code
.coord_single_range_expand_withdash Source code
.copy_DT Source code
.cov_process_regions Source code
.fetch_AH Source code
.fetch_AH_cache_loc 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
.fix_gtf 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_nmd Source code
.gen_nmd_determine Source code
.gen_nmd_determine_build_introns_upstream 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
.getGeneList Source code
.get_NxtIRFcore_cache Source code
.get_cache_file_path Source code
.get_reference_data Source code
.gmr_check_params Source code
.grDT Source code
.grlGaps Source code
.gtf_get_genome_style Source code
.irfinder_run_featureCounts Source code
.irfinder_run_single Source code
.irfinder_validate_args Source code
.is_AH_pattern Source code
.loadTranscripts Source code
.loadViewRef Source code
.log Source code
.makeSE_colData_clean Source code
.makeSE_iterate_IR Source code
.makeSE_iterate_IR_retrieve_excluded_introns Source code
.makeSE_iterate_IR_select_events Source code
.makeSE_validate_args Source code
.make_path_relative Source code
.nxtcat Source code
.overlaps_exon_island Source code
.parse_valid_file Source code
.prepare_covplot_data 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
.runFilter_anno_mxe Source code
.runFilter_anno_mxe_gr_casette Source code
.runFilter_anno_nmd Source code
.runFilter_anno_pc 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_IRFinder Source code
.run_IRFinder_GenerateMapReads Source code
.run_IRFinder_MapExclusionRegions Source code
.se_to_nxtse Source code
.semi_join_DT Source code
.split_vector 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_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-methods Man page
BAM2COV Man page Source code
BuildReference Man page Source code
BuildReference_Full Man page Source code
CollateData Man page Source code
CoordToGR Man page Source code
Coverage Man page
DESeq_ASE Man page Source code
DoubleExpSeq_ASE Man page Source code
Find_Bams Man page Source code
Find_FASTQ Man page Source code
Find_IRFinder_Output Man page Source code
Find_Samples Man page Source code
GetCoverage Man page Source code
GetCoverageBins Man page Source code
GetCoverageRegions Man page Source code
GetCoverage_DF Man page Source code
GetNonPolyARef Man page Source code
GetReferenceResource Man page Source code
Get_GTF_file Source code
Get_Genome Source code
Has_OpenMP Source code
IRF_BAM2COV Source code
IRF_Check_Cov Source code
IRF_Cov_Seqnames Source code
IRF_GenerateMappabilityReads Source code
IRF_GenerateMappabilityRegions Source code
IRF_RLEList_From_Cov Source code
IRF_RLE_From_Cov Source code
IRF_gunzip Source code
IRF_gunzip_DF Source code
IRF_main Source code
IRF_main_multi Source code
IRFinder Man page Source code
IsCOV Man page Source code
MakeSE Man page Source code
Mappability-methods Man page
Mappability_CalculateExclusions Man page Source code
Mappability_GenReads Man page Source code
NxtFilter Man page Source code
NxtFilter-class Man page
NxtIRF_example_NxtSE Man page Source code
NxtIRF_example_bams Man page Source code
NxtIRFcore-package Man page
NxtSE Man page Source code
NxtSE-class Man page
NxtSE-methods Man page
Plot_Coverage Man page Source code
Plot_Genome Man page Source code
Run_NxtIRF_Filters Man page
SE_charbound Source code
STAR-methods Man page
STAR_Mappability Man page Source code
STAR_align_experiment Man page Source code
STAR_align_fastq Man page Source code
STAR_buildRef Man page Source code
STAR_version Man page Source code
Test_OpenMP_For Source code
[,NxtSE,ANY,ANY,ANY-method Man page
[<-,NxtSE,ANY,ANY,NxtSE-method Man page
apply_filters Man page Source code
as_egg_ggplot Man page Source code
assay_withDimnames Source code
cbind,NxtSE-method Man page
coerce,SummarizedExperiment,NxtSE-method Man page
covfile Man page
covfile,NxtSE-method Man page
covfile<- Man page
covfile<-,NxtSE-method Man page
dash_progress Source code
dash_withProgress 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-NxtIRF-data Man page
get_default_filters Man page Source code
get_multi_DT_from_gz Source code
is.nan.data.frame Source code
is_valid Source code
limma_ASE Man page Source code
make_diagonal Man page Source code
make_matrix Man page Source code
make_plot_data Man page
rbind,NxtSE-method Man page
realize_NxtSE Man page
realize_NxtSE,NxtSE-method Man page
ref Man page
ref,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
set_dimnames Source code
simplify_NULL_dimnames Source code
theme_white Man page
theme_white_legend Man page
theme_white_legend_plot_track Man page
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
vector_withDimnames Source code
alexchwong/NxtIRFcore documentation built on Oct. 31, 2022, 9:14 a.m.

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