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Open Source Science

BiocHubsShiny

https://github.com/bioconductor/biochubsshiny

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.9%) to scientific vocabulary

Keywords from Contributors

bioconductor-package nci-itcr r01ca230551 u24ca289073 genomics immune-repertoire mutations data-structure copynumber core-package
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 4 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog

README.md

BiocHubsShiny

The BiocHubsShiny package allows users to visually explore the AnnotationHub and ExperimentHub resources via shiny. It provides a tabular display of the available resources with the ability to filter and search through the column fields.

Installation

``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("BiocHubsShiny") ```

Loading the package

r library(BiocHubsShiny)

Display of resources

Resources are displayed interactively using the eponymous function:

r BiocHubsShiny()

Filtering

You can filter by any of the columns in the table. For example, you can search for ‘Mus musculus’ to get resources only for that species:

Selection

Click on the rows to select the resources. They will show up as highlighted rows.

Import

Once the selection is highlighted, the code at the bottom of the app will be updated to show the commands for entering (reproducibly) into the R session.

Session Info

``` r sessionInfo()

> R Under development (unstable) (2025-04-02 r88102)

> Platform: x86_64-pc-linux-gnu

> Running under: Ubuntu 22.04.5 LTS

>

> Matrix products: default

> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0

> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 LAPACK version 3.10.0

>

> locale:

> [1] LCCTYPE=enUS.UTF-8 LC_NUMERIC=C

> [3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8

> [5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8

> [7] LCPAPER=enUS.UTF-8 LC_NAME=C

> [9] LCADDRESS=C LCTELEPHONE=C

> [11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

>

> time zone: America/New_York

> tzcode source: system (glibc)

>

> attached base packages:

> [1] stats graphics grDevices utils datasets methods base

>

> other attached packages:

> [1] BiocHubsShiny1.7.5 shiny1.10.0 colorout_1.2-2

>

> loaded via a namespace (and not attached):

> [1] rappdirs0.3.3 generics0.1.3 BiocVersion_3.21.1

> [4] RSQLite2.3.9 digest0.6.37 magrittr_2.0.3

> [7] evaluate1.0.3 fastmap1.2.0 blob_1.2.4

> [10] jsonlite2.0.0 AnnotationHub3.15.1 AnnotationDbi_1.69.0

> [13] GenomeInfoDb1.43.4 DBI1.2.3 promises_1.3.2

> [16] BiocManager1.30.25 httr1.4.7 UCSC.utils_1.3.1

> [19] Biostrings2.75.4 codetools0.2-20 httr2_1.1.2

> [22] cli3.6.4 crayon1.5.3 rlang_1.1.5

> [25] XVector0.47.2 dbplyr2.5.0 Biobase_2.67.0

> [28] bit644.6.0-1 cachem1.1.0 yaml_2.3.10

> [31] tools4.6.0 memoise2.0.1 dplyr_1.1.4

> [34] GenomeInfoDbData1.2.14 httpuv1.6.15 filelock_1.0.3

> [37] ExperimentHub2.15.1 BiocGenerics0.53.6 curl_6.2.2

> [40] png0.1-8 vctrs0.6.5 R6_2.6.1

> [43] mime0.13 stats44.6.0 BiocFileCache_2.15.1

> [46] lifecycle1.0.4 KEGGREST1.47.1 IRanges_2.41.3

> [49] S4Vectors0.45.4 bit4.6.0 pkgconfig_2.0.3

> [52] pillar1.10.1 later1.4.1 glue_1.8.0

> [55] Rcpp1.0.14 xfun0.52 tibble_3.2.1

> [58] tidyselect1.2.1 rstudioapi0.17.1 knitr_1.50

> [61] xtable1.8-4 htmltools0.5.8.1 rmarkdown_2.29

> [64] compiler_4.6.0

```

Owner

  • Name: Bioconductor
  • Login: Bioconductor
  • Kind: organization

Software for the analysis and comprehension of high-throughput genomic data

GitHub Events

Total
  • Member event: 1
  • Push event: 15
  • Create event: 3
Last Year
  • Member event: 1
  • Push event: 15
  • Create event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 58
  • Total Committers: 5
  • Avg Commits per committer: 11.6
  • Development Distribution Score (DDS): 0.155
Past Year
  • Commits: 36
  • Committers: 3
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.111
Top Committers
Name Email Commits
LiNk-NY m****z@r****g 49
LiNk-NY m****s@r****g 4
J Wokaty j****y@s****u 2
J Wokaty j****y 2
Marcel Ramos L****Y 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 2 sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: about 12 hours
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • vjcitn (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 6,096 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: BiocHubsShiny

View AnnotationHub and ExperimentHub Resources Interactively

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 6,096 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 19.8%
Average: 29.2%
Stargazers count: 33.2%
Downloads: 93.1%
Maintainers (1)
marcel.ramos@sph.cuny.edu
Last synced: 10 months ago