Data

Tools

Indexes

Applications

Experiments

Open Source Science

iSEE

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

https://github.com/isee/isee

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
    4 of 15 committers (26.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization

Keywords from Contributors

bioconductor-package bioconductor core-package u24ca289073 gene ontology bioinformatics rnaseq mass-spectrometry deseq2
Last synced: 6 months ago · JSON representation

Repository

R/shiny interface for interactive visualization of data in SummarizedExperiment objects

Basic Info
Statistics
  • Stars: 228
  • Watchers: 16
  • Forks: 43
  • Open Issues: 29
  • Releases: 1
Topics
clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization
Created about 8 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License Code of conduct

README.md

iSEE - The interactive SummarizedExperiment Explorer

GitHub issues GitHub pulls Lifecycle: stable R-CMD-check-bioc Codecov test coverage <!-- badges: end -->

Bioconductor release status

| Branch | R CMD check | Last updated | |:----------------:|:----------------:|:------------:| | devel | Bioconductor-devel Build Status | | | release | Bioconductor-release Build Status | |

Overview

The iSEE package provides an interactive user interface for exploring data in objects derived from the SummarizedExperiment class. Particular focus is given to single-cell data stored in the SingleCellExperiment derived class. The user interface is implemented with RStudio's Shiny, with a multi-panel setup for ease of navigation.

This initiative was proposed at the European Bioconductor Meeting in Cambridge, 2017. Current contributors include:

Figure 1. _iSEE_ uses a customisable multi-panel layout.

Installation

iSEE can be easily installed from Bioconductor using BiocManager::install():

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

or also...

BiocManager::install("iSEE", dependencies = TRUE) ```

Setting dependencies = TRUE should ensure that all packages, including the ones in the Suggests: field of the DESCRIPTION, are installed - this can be essential if you want to reproduce the code in the vignette, for example.

Functionalities

Click to expand the list of features available in iSEE applications. ### General * Multiple interactive plot types with selectable points. * Interactive tables with selectable rows. * Coloring of samples and features by metadata or expression data. * Zooming to a plot subregion. * Transmission of point selections between panels to highlight, color, or restrict data points in the receiving panel(s). * Lasso point selection to define complex shapes. ### Sample-level visualization The _iSEE_ user interface currently contains the following components where each data point represents a single biological sample: * **Reduced dimension plot**: Scatter plot of reduced dimensionality data. * **Column data plot**: Adaptive plot of any one or two sample metadata. A scatter, violin, or square design is dynamically applied according to the continuous or discrete nature of the metadata. * **Feature assay plot**: Adaptive plot of expression data across samples for any two features or one feature against one sample metadata. * **Column data table**: Table of sample metadata. ### Feature-level visualization The _iSEE_ user interface currently contains the following components where each data point represents a genomic feature: * **Row data plot**: Adaptive plot of any two feature metadata. A scatter, violin, or square design is dynamically applied according to the continuous or discrete nature of the metadata. * **Sample assay plot**: Adaptive plot of expression data across features for any two samples or one sample against one feature metadata. * **Row data table**: Table of feature metadata. ### Integrated visualization The _iSEE_ user interface contains the following components that integrate sample and feature information: * **Complex heatmap plot**: Visualize multiple features across multiple samples annotated with sample metadata. ### Custom panels The _iSEE_ API allows users to programmatically define their own plotting and table panels. See the section [Extending _iSEE_](#extending-isee) further below. ### Miscellaneous * The _iSEE_ user interface continually tracks the code corresponding to all visible plotting panels. This code is rendered in a [shinyAce](https://cran.r-project.org/web/packages/shinyAce/index.html) text editor and can be copy-pasted into R scripts for customization and further use. * Speech recognition can be enabled to control the user interface using voice commands.

Want to try iSEE?

We set up instances of iSEE applications running on diverse types of datasets at those addresses:

  • http://shiny.imbei.uni-mainz.de:3838/iSEE
  • https://marionilab.cruk.cam.ac.uk/iSEE_allen
  • https://marionilab.cruk.cam.ac.uk/iSEE_tcga
  • https://marionilab.cruk.cam.ac.uk/iSEE_pbmc4k
  • https://marionilab.cruk.cam.ac.uk/iSEE_cytof

Please keep in mind that those public instances are for trial purposes only; yet they demonstrate how you or your system administrator can setup iSEE for analyzing or sharing your precomputed SummarizedExperiment/SingleCellExperiment object.

Extending iSEE

If you want to extend the functionality of iSEE, you can create custom panels which add new possibilities to interact with your data. Custom panels can be defined in independent R packages that include iSEE in the Imports: sections of their DESCRIPTION file. You can find a collection of working examples of how to do it in iSEEu. Feel free to contact the developing team, should you need some clarifications on how iSEE works internally.

Code of Conduct

Please note that the iSEE project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Owner

  • Name: iSEE everything
  • Login: iSEE
  • Kind: organization

GitHub Events

Total
  • Issues event: 12
  • Watch event: 6
  • Delete event: 6
  • Issue comment event: 55
  • Push event: 25
  • Pull request review event: 4
  • Pull request review comment event: 3
  • Pull request event: 9
  • Fork event: 2
  • Create event: 7
Last Year
  • Issues event: 12
  • Watch event: 6
  • Delete event: 6
  • Issue comment event: 55
  • Push event: 25
  • Pull request review event: 4
  • Pull request review comment event: 3
  • Pull request event: 9
  • Fork event: 2
  • Create event: 7

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 2,719
  • Total Committers: 15
  • Avg Commits per committer: 181.267
  • Development Distribution Score (DDS): 0.586
Past Year
  • Commits: 15
  • Committers: 4
  • Avg Commits per committer: 3.75
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
Kevin Rue-Albrecht k****7@g****m 1,125
LTLA i****s@g****m 554
Aaron Lun a****n@w****u 407
Aaron Lun a****n@c****k 253
Federico Marini m****f@u****e 171
Charlotte Soneson c****n@g****m 132
Aaron Lun L****A 44
Nitesh Turaga n****a@g****m 14
Your Name y****u@e****m 7
J Wokaty j****y@s****u 4
vobencha v****n@r****g 2
J Wokaty j****y 2
vobencha v****a@g****m 2
Kayla-Morrell k****l@r****g 1
Leonardo Collado-Torres l****r@g****m 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 2 sph.cuny.edu: 1 uni-mainz.de: 1 cruk.cam.ac.uk: 1 wehi.edu.au: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 87
  • Total pull requests: 72
  • Average time to close issues: about 1 year
  • Average time to close pull requests: about 1 month
  • Total issue authors: 30
  • Total pull request authors: 7
  • Average comments per issue: 3.25
  • Average comments per pull request: 1.11
  • Merged pull requests: 66
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 12
  • Pull requests: 19
  • Average time to close issues: 6 days
  • Average time to close pull requests: 2 days
  • Issue authors: 7
  • Pull request authors: 5
  • Average comments per issue: 2.92
  • Average comments per pull request: 1.05
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kevinrue (20)
  • daymecita (9)
  • csoneson (8)
  • LTLA (7)
  • lcolladotor (4)
  • lee-t (4)
  • rerigby (3)
  • RiboRings (3)
  • daymegr (2)
  • cathalgking (2)
  • tomsing1 (2)
  • jma1991 (2)
  • dominikburri (2)
  • malcook (2)
  • kniekamp19 (1)
Pull Request Authors
  • kevinrue (45)
  • csoneson (18)
  • LTLA (16)
  • federicomarini (13)
  • RiboRings (3)
  • lcolladotor (1)
  • rh680 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • bioconductor 46,904 total
  • Total dependent packages: 8
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: iSEE

Interactive SummarizedExperiment Explorer

  • Versions: 5
  • Dependent Packages: 8
  • Dependent Repositories: 0
  • Downloads: 46,904 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 0.8%
Forks count: 1.0%
Average: 5.5%
Downloads: 25.7%
Maintainers (1)
kevinrue67@gmail.com
Last synced: 7 months ago
proxy.golang.org: github.com/iSEE/iSEE
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/isee/isee
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago

Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/publish_docker.yaml actions
  • actions/checkout v1 composite
  • elgohr/Publish-Docker-Github-Action master composite
DESCRIPTION cran
  • SingleCellExperiment * depends
  • SummarizedExperiment * depends
  • BiocGenerics * imports
  • ComplexHeatmap * imports
  • DT * imports
  • S4Vectors * imports
  • circlize * imports
  • colourpicker * imports
  • ggplot2 * imports
  • ggrepel * imports
  • grDevices * imports
  • graphics * imports
  • grid * imports
  • igraph * imports
  • methods * imports
  • mgcv * imports
  • rintrojs * imports
  • shiny * imports
  • shinyAce * imports
  • shinyWidgets * imports
  • shinydashboard * imports
  • shinyjs * imports
  • stats * imports
  • utils * imports
  • vipor * imports
  • viridisLite * imports
  • BiocStyle * suggests
  • DelayedArray * suggests
  • HDF5Array * suggests
  • RColorBrewer * suggests
  • TENxPBMCData * suggests
  • covr * suggests
  • htmltools * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • scRNAseq * suggests
  • scater * suggests
  • testthat * suggests
  • viridis * suggests
Dockerfile docker
  • bioconductor/bioconductor_docker devel build