Package: Ularcirc 1.23.0

David Humphreys

Ularcirc: Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.

Authors:David Humphreys [aut, cre]

Ularcirc_1.23.0.tar.gz
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Ularcirc.pdf |Ularcirc.html✨
Ularcirc/json (API)
NEWS

# Install 'Ularcirc' in R:

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

On BioConductor:Ularcirc-1.23.0(bioc 3.20)Ularcirc-1.22.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

11 exports 0.91 score 151 dependencies 2 mentions

Last updated 2 months agofrom:8ca4b0faa9

Exports:BSJ_details bsj_fastq_generate bsj_to_circRNA_sequence chimericStats Compatible_Annotation_DBs FilterChimericJuncs loadSTAR_chimeric plot_AllJunctions RAD_score SelectUniqueJunctions Ularcirc

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome bslib cachem cli codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest dplyr DT evaluate fansi farver fastmap filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggplotify ggrepel glue gridGraphics gsubfn gtable highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime mirbase.db moments munsell nlme openssl Organism.dplyr pillar pkgconfig plogr plotgardener plyranges png promises proto purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sass scales shiny shinydashboard shinyFiles shinyjs snow sourcetools SparseArray strawr stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XML xtable XVector yaml yulab.utils zlibbioc

Ularcirc: A shiny application for canonical and back splicing analysis

David Humphreys, Nicolas Fossat, Patrick Tam, Joshua Ho

Rendered fromUlarcirc.Rmdusingknitr::rmarkdownon Jun 17 2024.

Last update: 2019-10-24
Started: 2019-08-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BSJ_details This function returns details of a BSJ string and returns a list of coordinates. Can accept two different formats, Ularcirc or generic.	BSJ_details
bsj_fastq_generate	bsj_fastq_generate
bsj_to_circRNA_sequence	bsj_to_circRNA_sequence
chimericFilters	chimericFilters
chimericStats	chimericStats
Compatible_Annotation_DBs	Compatible_Annotation_DBs
Wrapper function for Ularcirc shiny app which expects a list of objects to be returned	FilterChimeric_Ularcirc
FilterChimericJuncs	FilterChimericJuncs
Grab_BS_Junc_Sequence	Junction_Sequence_from_Genome
loadSTAR_chimeric	loadSTAR_chimeric
plot_AllJunctions	plot_AllJunctions
RAD_score	RAD_score
SelectUniqueJunctions	SelectUniqueJunctions
sequence_from_exon_coords	sequence_from_exon_coords
Ularcirc	Ularcirc