A B C D E F G I J M N P R S T U V misc
| SpliceWiz-package | SpliceWiz: efficient and precise alternative splicing analysis in R |
| addPSI_edgeR | Using Generalised linear models to analyse differential ASEs using edgeR |
| applyFilters | Filtering for IR and Alternative Splicing Events |
| ASE-GLM-edgeR | Using Generalised linear models to analyse differential ASEs using edgeR |
| ASE-methods | Differential Alternative Splicing Event analysis |
| ASEFilter | SpliceWiz filters to remove low-confidence alternative splicing and intron retention events |
| ASEFilter-class | SpliceWiz filters to remove low-confidence alternative splicing and intron retention events |
| ASE_DESeq | Differential Alternative Splicing Event analysis |
| ASE_DoubleExpSeq | Differential Alternative Splicing Event analysis |
| ASE_edgeR | Differential Alternative Splicing Event analysis |
| ASE_edgeR_timeseries | Differential Alternative Splicing Event analysis |
| ASE_limma | Differential Alternative Splicing Event analysis |
| ASE_limma_timeseries | Differential Alternative Splicing Event analysis |
| BAM2COV | Runs the OpenMP/C++ based SpliceWiz algorithm |
| Build-Reference-methods | Builds reference files used by SpliceWiz |
| buildFullRef | Builds reference files used by SpliceWiz |
| buildRef | Builds reference files used by SpliceWiz |
| calculateMappability | Calculate low mappability genomic regions |
| cbind-method | The NxtSE class |
| coerce-method | The NxtSE class |
| collateData | Collates a dataset from (processBAM) output files of individual samples |
| condition | Versatile coverage plots for SpliceWiz |
| condition-method | Versatile coverage plots for SpliceWiz |
| coord2GR | Converts genomic coordinates into a GRanges object |
| covDataObject-class | Container to hold raw data for SpliceWiz coverage plots |
| Coverage | Calls SpliceWiz's C++ function to retrieve coverage from a COV file |
| covfile | The NxtSE class |
| covfile-method | The NxtSE class |
| covfile<- | The NxtSE class |
| covfile<--method | The NxtSE class |
| covPlotly-class | Container for plotly-based coverage plots |
| covPlotObject-class | Versatile coverage plots for SpliceWiz |
| down_exc | The NxtSE class |
| down_exc-method | The NxtSE class |
| down_exc<- | The NxtSE class |
| down_exc<--method | The NxtSE class |
| down_inc | The NxtSE class |
| down_inc-method | The NxtSE class |
| down_inc<- | The NxtSE class |
| down_inc<--method | The NxtSE class |
| example-SpliceWiz-data | SpliceWiz Example BAMs and NxtSE Experiment Object |
| extract_gene_ids_for_GO | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events |
| findBAMS | Convenience Function to (recursively) find all files in a folder. |
| findFASTQ | Convenience Function to (recursively) find all files in a folder. |
| findSamples | Convenience Function to (recursively) find all files in a folder. |
| findSpliceWizOutput | Convenience Function to (recursively) find all files in a folder. |
| fitASE_edgeR | Using Generalised linear models to analyse differential ASEs using edgeR |
| fitASE_edgeR_custom | Using Generalised linear models to analyse differential ASEs using edgeR |
| Gene-ontology-methods | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events |
| generateSyntheticReads | Calculate low mappability genomic regions |
| getAvailableGO | Builds reference files used by SpliceWiz |
| getCoverage | Calls SpliceWiz's C++ function to retrieve coverage from a COV file |
| getCoverageBins | Calls SpliceWiz's C++ function to retrieve coverage from a COV file |
| getCoverageData | Container to hold raw data for SpliceWiz coverage plots |
| getCoverageRegions | Calls SpliceWiz's C++ function to retrieve coverage from a COV file |
| getCoverage_DF | Calls SpliceWiz's C++ function to retrieve coverage from a COV file |
| getDefaultFilters | Filtering for IR and Alternative Splicing Events |
| getExonRanges | Container for plotly-based coverage plots |
| getExonRanges-method | Container for plotly-based coverage plots |
| getGenomeData | Container to hold raw data for SpliceWiz coverage plots |
| getNonPolyARef | Builds reference files used by SpliceWiz |
| getPlotObject | Versatile coverage plots for SpliceWiz |
| getResources | Builds reference files used by SpliceWiz |
| goASE | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events |
| goGenes | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events |
| Graphics-User-Interface | Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard |
| GUI | Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard |
| isCOV | Validates the given file as a valid COV file |
| junc_counts | The NxtSE class |
| junc_counts-method | The NxtSE class |
| junc_counts_uns | The NxtSE class |
| junc_counts_uns-method | The NxtSE class |
| junc_gr | The NxtSE class |
| junc_gr-method | The NxtSE class |
| junc_PSI | The NxtSE class |
| junc_PSI-method | The NxtSE class |
| makeMatrix | Construct data of percent-spliced-in (PSI) matrices and group-average PSIs |
| makeMeanPSI | Construct data of percent-spliced-in (PSI) matrices and group-average PSIs |
| makeSE | Imports a collated dataset into the R session as an NxtSE object |
| make_plot_data | Construct data of percent-spliced-in (PSI) matrices and group-average PSIs |
| Mappability-methods | Calculate low mappability genomic regions |
| NxtSE | The NxtSE class |
| NxtSE-class | The NxtSE class |
| NxtSE-methods | The NxtSE class |
| plotAnnoTrack | Container to hold raw data for SpliceWiz coverage plots |
| plotCoverage | RNA-seq Coverage Plots and Genome Tracks |
| plotGenome | RNA-seq Coverage Plots and Genome Tracks |
| plotGO | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events |
| plotView | Versatile coverage plots for SpliceWiz |
| processBAM | Runs the OpenMP/C++ based SpliceWiz algorithm |
| rbind-method | The NxtSE class |
| realize_NxtSE | The NxtSE class |
| realize_NxtSE-method | The NxtSE class |
| ref | The NxtSE class |
| ref-method | The NxtSE class |
| row_gr | The NxtSE class |
| row_gr-method | The NxtSE class |
| runFilter | Filtering for IR and Alternative Splicing Events |
| Run_SpliceWiz_Filters | Filtering for IR and Alternative Splicing Events |
| sampleQC | The NxtSE class |
| sampleQC-method | The NxtSE class |
| sampleQC<- | The NxtSE class |
| sampleQC<--method | The NxtSE class |
| setResolution | Container for plotly-based coverage plots |
| setResolution-method | Container for plotly-based coverage plots |
| setSWthreads | Sets the number of threads used by SpliceWiz |
| showEvents | Container to hold raw data for SpliceWiz coverage plots |
| showEvents-method | Container to hold raw data for SpliceWiz coverage plots |
| showExons | Container for plotly-based coverage plots |
| showExons-method | Container for plotly-based coverage plots |
| sourcePath | The NxtSE class |
| sourcePath-method | The NxtSE class |
| spliceWiz | Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard |
| SpliceWiz_example_bams | SpliceWiz Example BAMs and NxtSE Experiment Object |
| SpliceWiz_example_NxtSE | SpliceWiz Example BAMs and NxtSE Experiment Object |
| STAR-methods | STAR wrappers for building reference for STAR, and aligning RNA-sequencing |
| STAR_alignExperiment | STAR wrappers for building reference for STAR, and aligning RNA-sequencing |
| STAR_alignReads | STAR wrappers for building reference for STAR, and aligning RNA-sequencing |
| STAR_buildGenome | STAR wrappers for building reference for STAR, and aligning RNA-sequencing |
| STAR_buildRef | STAR wrappers for building reference for STAR, and aligning RNA-sequencing |
| STAR_loadGenomeGTF | STAR wrappers for building reference for STAR, and aligning RNA-sequencing |
| STAR_mappability | STAR wrappers for building reference for STAR, and aligning RNA-sequencing |
| STAR_version | STAR wrappers for building reference for STAR, and aligning RNA-sequencing |
| subset_EventNames_by_GO | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events |
| testASE_edgeR | Using Generalised linear models to analyse differential ASEs using edgeR |
| theme_white | ggplot2 themes |
| theme_white_legend | ggplot2 themes |
| theme_white_legend_plot_track | ggplot2 themes |
| tracks | Versatile coverage plots for SpliceWiz |
| tracks-method | Versatile coverage plots for SpliceWiz |
| update_NxtSE | The NxtSE class |
| update_NxtSE-method | The NxtSE class |
| up_exc | The NxtSE class |
| up_exc-method | The NxtSE class |
| up_exc<- | The NxtSE class |
| up_exc<--method | The NxtSE class |
| up_inc | The NxtSE class |
| up_inc-method | The NxtSE class |
| up_inc<- | The NxtSE class |
| up_inc<--method | The NxtSE class |
| View-Reference-methods | View SpliceWiz Reference in read-able data frames |
| viewASE | View SpliceWiz Reference in read-able data frames |
| viewExons | View SpliceWiz Reference in read-able data frames |
| viewGenes | View SpliceWiz Reference in read-able data frames |
| viewGO | View SpliceWiz Reference in read-able data frames |
| viewIntrons | View SpliceWiz Reference in read-able data frames |
| viewIR | View SpliceWiz Reference in read-able data frames |
| viewIR_NMD | View SpliceWiz Reference in read-able data frames |
| viewProteins | View SpliceWiz Reference in read-able data frames |
| viewTranscripts | View SpliceWiz Reference in read-able data frames |
| [-method | The NxtSE class |
| [<--method | The NxtSE class |