Package: maser 1.25.0

Diogo F.T. Veiga

maser: Mapping Alternative Splicing Events to pRoteins

This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.

Authors:Diogo F.T. Veiga [aut, cre]

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maser.pdf |maser.html✨
maser/json (API)
NEWS

# Install 'maser' in R:

install.packages('maser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/diogoveiga/maser/issues

On BioConductor:maser-1.25.0(bioc 3.21)maser-1.24.0(bioc 3.20)

alternativesplicing transcriptomics visualization

6.69 score 18 stars 15 scripts 379 downloads 3 mentions 21 exports 154 dependencies

Last updated 23 days agofrom:390af674b6. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 19 2024
R-4.5-win	NOTE	Nov 19 2024
R-4.5-linux	NOTE	Nov 19 2024
R-4.4-win	NOTE	Nov 19 2024
R-4.4-mac	NOTE	Nov 19 2024
R-4.3-win	NOTE	Nov 19 2024
R-4.3-mac	NOTE	Nov 19 2024

Exports:annotation availableFeaturesUniprotKB boxplot_PSI_levels counts display dotplot filterByCoverage filterByEventId geneEvents mapProteinFeaturesToEvents mapTranscriptsToEvents maser pca plotGenePSI plotTranscripts plotUniprotKBFeatures PSI splicingDistribution summary topEvents volcano

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr DT ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr plyr png prettyunits progress promises ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

Introduction

Diogo Veiga

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2018-07-20
Started: 2018-02-28

Mapping protein features to splicing events

Diogo Veiga

Rendered fromProtein_mapping.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2018-07-20
Started: 2018-03-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Retrieve annotation of splicing events from a maser object.	annotation,Maser-method
Query available human protein features in UniprotKB.	availableFeaturesUniprotKB
Boxplots of PSI distributions by splicing type.	boxplot_PSI_levels
Retrieve raw read counts values from a maser object.	counts,Maser-method
Visualization of splicing events annotation using an interactive data table.	display
Dotplot representation of splicing events.	dotplot
Filter splicing events based on coverage.	filterByCoverage
Filter splicing events based on event identifier and type.	filterByEventId
Retrieve splicing events for a given gene.	geneEvents
Retrieve genomic ranges of splicing events from a maser object.	granges,Maser-method
Mapping of splice events to UniprotKB protein features.	mapProteinFeaturesToEvents
Mapping of splice events to Ensembl transcripts.	mapTranscriptsToEvents
Create a maser object by importing rMATS splicing events.	maser
S4 class to represent splicing events imported from rMATS.	Maser-class
Prinicipal component analysis of PSI distributions.	pca
Boxplots of Percent spliced-in levels for gene events.	plotGenePSI
Mapping and visualization of Ensembl transcripts affected by splicing.	plotTranscripts
Mapping and visualization of UniprotKB protein features affected by splicing.	plotUniprotKBFeatures
Retrieve PSI (percent spliced in) values from a maser object.	PSI
Retrieve PSI (percent spliced in) values from a maser object.	PSI,Maser,character-method
Proportion of events by splicing type.	splicingDistribution
Retrieve rMATS stats of differential splicing from a maser object.	summary,Maser-method
Filter splicing events based on false discovery rate and PSI change.	topEvents
Volcano plot of splicing events.	volcano