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 |
applyFilters | Filtering for IR and Alternative Splicing Events |
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_limma | Differential Alternative Splicing Event analysis |
ASE_satuRn | Differential Alternative Splicing Event analysis |
as_ggplot_cov | RNA-seq Coverage Plots and Genome Tracks |
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 |
coord2GR | Converts genomic coordinates into a GRanges object |
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 |
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 |
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. |
generateSyntheticReads | Calculate low mappability genomic regions |
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 |
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 |
getNonPolyARef | Builds reference files used by SpliceWiz |
getResources | Builds reference files used by SpliceWiz |
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_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 |
plotCoverage | RNA-seq Coverage Plots and Genome Tracks |
plotGenome | RNA-seq Coverage Plots and Genome Tracks |
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 |
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 |
setSWthreads | Sets the number of threads used by SpliceWiz |
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_buildRef | 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 |
theme_white | ggplot2 themes |
theme_white_legend | ggplot2 themes |
theme_white_legend_plot_track | ggplot2 themes |
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 |
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 |