Package: Ularcirc 1.31.0

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_1.31.0.tar.gz
Ularcirc_1.31.0.zip(r-4.7)Ularcirc_1.31.0.zip(r-4.6)Ularcirc_1.31.0.zip(r-4.5)
Ularcirc_1.31.0.tgz(r-4.6-any)Ularcirc_1.31.0.tgz(r-4.5-any)
Ularcirc_1.31.0.tar.gz(r-4.7-any)Ularcirc_1.31.0.tar.gz(r-4.6-any)
Ularcirc_1.31.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Ularcirc/json (API)

# Install 'Ularcirc' in R:

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

On BioConductor:Ularcirc-1.31.0(bioc 3.24)Ularcirc-1.30.0(bioc 3.23)

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

datarepresentation visualization genetics sequencing annotation coverage alternativesplicing differentialsplicing

4.70 score 6 scripts 358 downloads 2 mentions 13 exports 148 dependencies

Last updated from:9e0304952e. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	303
linux-devel-x86_64	WARNING	405
source / vignettes	OK	389
linux-release-x86_64	WARNING	429
macos-release-arm64	WARNING	257
macos-oldrel-arm64	WARNING	188
windows-devel	WARNING	271
windows-release	WARNING	284
windows-oldrel	WARNING	264
wasm-release	OK	276

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

Dependencies:abind AnnotationDbi AnnotationHub askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome bslib cachem cigarillo cli codetools commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray digest dir.expiry dplyr DT evaluate 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 httr2 IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime moments openssl otel pillar pkgconfig 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 S7 sass scales Seqinfo 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

Ularcirc: A shiny application for canonical and back splicing analysis

Rendered fromUlarcirc.Rmdusingknitr::rmarkdown

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
circSequence This function returns pre-defined full length circRNA sequences.	circSequence
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
load_miRBase_fasta This function extracts species specific mirbase sequences as a Biostrings RNAstringset.	load_miRBase_fasta
loadSTAR_chimeric	loadSTAR_chimeric
miR_binding_site_Analysis This function analyses a genomic (RNA or DNA) sequence for matching miRNA seed sequences.	miR_binding_site_Analysis
plot_AllJunctions	plot_AllJunctions
RAD_score	RAD_score
SelectUniqueJunctions	SelectUniqueJunctions
sequence_from_exon_coords	sequence_from_exon_coords
Ularcirc	Ularcirc