Package: JBrowseR 0.10.2

Colin Diesh

JBrowseR: An R Interface to the JBrowse 2 Genome Browser

Provides an R interface to the JBrowse 2 genome browser. Enables embedding a JB2 genome browser in a Shiny app or R Markdown document. The browser can also be launched from an interactive R console. The browser can be loaded with a variety of common genomics data types, and can be used with a custom theme.

Authors:Elliot Hershberg [aut], Colin Diesh [aut, cre], the JBrowse 2 Team [aut]

JBrowseR_0.10.2.tar.gz
JBrowseR_0.10.2.zip(r-4.5)JBrowseR_0.10.2.zip(r-4.4)JBrowseR_0.10.2.zip(r-4.3)
JBrowseR_0.10.2.tgz(r-4.4-any)JBrowseR_0.10.2.tgz(r-4.3-any)
JBrowseR_0.10.2.tar.gz(r-4.5-noble)JBrowseR_0.10.2.tar.gz(r-4.4-noble)
JBrowseR_0.10.2.tgz(r-4.4-emscripten)JBrowseR_0.10.2.tgz(r-4.3-emscripten)
JBrowseR.pdf |JBrowseR.html✨
JBrowseR/json (API)
NEWS

# Install 'JBrowseR' in R:

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

Bug tracker:https://github.com/gmod/jbrowser/issues

On CRAN:

genomics reactjs rmarkdown shiny visualization

7.61 score 35 stars 1 packages 28 scripts 299 downloads 16 exports 61 dependencies

Last updated 8 months agofrom:981ad613b1. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 13 2024
R-4.5-win	NOTE	Oct 13 2024
R-4.5-linux	NOTE	Oct 13 2024
R-4.4-win	NOTE	Oct 13 2024
R-4.4-mac	NOTE	Oct 13 2024
R-4.3-win	NOTE	Oct 13 2024
R-4.3-mac	NOTE	Oct 13 2024

Exports:%>%assembly default_session JBrowseR JBrowseROutput json_config renderJBrowseR serve_data text_index theme track_alignments track_data_frame track_feature track_variant track_wiggle tracks

Dependencies:askpass base64enc bit bit64 bslib cachem cli clipr cpp11 crayon digest dplyr evaluate fansi fastmap fontawesome fs generics glue highr hms htmltools htmlwidgets httpuv ids jquerylib jsonlite knitr later lifecycle magrittr memoise mime openssl pillar pkgconfig prettyunits progress promises R6 rappdirs Rcpp reactR readr rlang rmarkdown sass stringi stringr sys tibble tidyselect tinytex tzdb utf8 uuid vctrs vroom withr xfun yaml

Advanced JSON tutorial

Rendered fromjson-tutorial.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2023-12-20
Started: 2021-02-18

Creating URLs

Rendered fromcreating-urls.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2021-02-18
Started: 2021-02-18

Custom browser tutorial

Rendered fromcustom-browser-tutorial.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2023-12-20
Started: 2021-02-17

Introduction to JBrowseR

Rendered fromJBrowseR.Rmdusingknitr::rmarkdownon Oct 13 2024.

Last update: 2021-02-23
Started: 2021-02-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create an assembly for a custom JBrowse view	assembly
Create a default session for a custom JBrowse view	default_session
R interface to JBrowse 2 genome browser	JBrowseR
Shiny bindings for JBrowseR	JBrowseR-shiny JBrowseROutput JBrowseR_html renderJBrowseR
Read in a JBrowse 2 JSON configuration file	json_config
Serve a local data directory for use with a browser	serve_data
Create configuration for a JBrowse 2 text index	text_index
Create a theme for a custom JBrowse 2 view	theme
Create an AlignmentsTrack for a custom JBrowse 2 view	track_alignments
Create a track from an R data frame for a custom JBrowse 2 view	track_data_frame
Create a FeatureTrack for a custom JBrowse 2 view	track_feature
Create a VariantTrack for a custom JBrowse 2 view	track_variant
Create a WiggleTrack for a custom JBrowse 2 view	track_wiggle
Create a set of tracks for a custom JBrowse 2 view	tracks