# Introduction to iSEEde

Kevin Rue-Albrecht1*

1University of Oxford

*kevin.rue-albrecht@imm.ox.ac.uk

#### 29 October 2024

#### Package

iSEEde 1.4.0

# 1 Basics

## 1.1 Install `iSEEde`

is an open-source statistical environment which can be easily modified to enhance its functionality via packages. iSEEde is an
package available via the Bioconductor repository for packages.
can be installed on any operating system from CRAN after which you can install iSEEde by using the following commands in your
session:

    if (!requireNamespace("BiocManager", quietly = TRUE)) {
        install.packages("BiocManager")
    }

    BiocManager::install("iSEEde")

    ## Check that you have a valid Bioconductor installation
    BiocManager::valid()

## 1.2 Required knowledge

iSEEde is based on many other packages and in particular on those that have implemented the infrastructure needed for dealing with omics data and interactive visualisation. That is, packages like SummarizedExperiment, SingleCellExperiment, iSEE and shiny.

If you are asking yourself the question “Where do I start using Bioconductor?” you might be interested in this blog post.

## 1.3 Asking for help

As package developers, we try to explain clearly how to use our packages and in which order to use the functions. But
and `Bioconductor` have a steep learning curve so it is critical to learn where to ask for help. The blog post quoted above mentions some but we would like to highlight the Bioconductor support site as the main resource for getting help: remember to use the `iSEEde` tag and check the older posts. Other alternatives are available such as creating GitHub issues and tweeting. However, please note that if you want to receive help you should adhere to the posting guidelines. It is particularly critical that you provide a small reproducible example and your session information so package developers can track down the source of the error.

## 1.4 Citing `iSEEde`

We hope that iSEEde will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!

    ## Citation info
    citation("iSEEde")
    #> To cite package 'iSEEde' in publications use:
    #>
    #>   Rue-Albrecht K (2024). _iSEEde: iSEE extension for panels related to differential
    #>   expression analysis_. doi:10.18129/B9.bioc.iSEEde
    #>   <https://doi.org/10.18129/B9.bioc.iSEEde>, R package version 1.4.0,
    #>   <https://bioconductor.org/packages/iSEEde>.
    #>
    #> A BibTeX entry for LaTeX users is
    #>
    #>   @Manual{,
    #>     title = {iSEEde: iSEE extension for panels related to differential expression analysis},
    #>     author = {Kevin Rue-Albrecht},
    #>     year = {2024},
    #>     note = {R package version 1.4.0},
    #>     url = {https://bioconductor.org/packages/iSEEde},
    #>     doi = {10.18129/B9.bioc.iSEEde},
    #>   }

# 2 Quick start to using to `iSEEde`

The example below demonstrates how to use iSEEde functionality in a simple differential expression workflow.

Specifically, the DESeq2 package is used to perform a simple differential expression analysis. Then, the results of one contrast – extracted using the function `DESeq2::results()` function – are embedded into the SummarizedExperiment object `airway` using the function `iSEEde::embedContrastResults()`. This ensures that the differential expression results for that contrast are accessible to specialised interactive panels in iSEE applications.

    library("iSEEde")
    library("airway")
    library("DESeq2")
    library("iSEE")

    # Example data ----

    data("airway")
    airway$dex <- relevel(airway$dex, "untrt")

    dds <- DESeqDataSet(airway, ~ 0 + dex + cell)

    dds <- DESeq(dds)
    res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt"))
    head(res_deseq2)
    #> log2 fold change (MLE): dextrt vs dexuntrt
    #> Wald test p-value: dextrt vs dexuntrt
    #> DataFrame with 6 rows and 6 columns
    #>                   baseMean log2FoldChange     lfcSE      stat      pvalue       padj
    #>                  <numeric>      <numeric> <numeric> <numeric>   <numeric>  <numeric>
    #> ENSG00000000003 708.602170     -0.3812539  0.100654 -3.787752 0.000152016 0.00128292
    #> ENSG00000000005   0.000000             NA        NA        NA          NA         NA
    #> ENSG00000000419 520.297901      0.2068127  0.112219  1.842944 0.065337213 0.19646961
    #> ENSG00000000457 237.163037      0.0379205  0.143445  0.264356 0.791505314 0.91141884
    #> ENSG00000000460  57.932633     -0.0881679  0.287142 -0.307054 0.758802543 0.89500551
    #> ENSG00000000938   0.318098     -1.3782416  3.499906 -0.393794 0.693733216         NA

    # iSEE / iSEEde ---

    airway <- embedContrastResults(res_deseq2, airway, name = "dex: trt vs untrt")
    contrastResults(airway)
    #> DataFrame with 63677 rows and 1 column
    #>                   dex: trt vs untrt
    #>                 <iSEEDESeq2Results>
    #> ENSG00000000003 <iSEEDESeq2Results>
    #> ENSG00000000005 <iSEEDESeq2Results>
    #> ENSG00000000419 <iSEEDESeq2Results>
    #> ENSG00000000457 <iSEEDESeq2Results>
    #> ENSG00000000460 <iSEEDESeq2Results>
    #> ...                             ...
    #> ENSG00000273489 <iSEEDESeq2Results>
    #> ENSG00000273490 <iSEEDESeq2Results>
    #> ENSG00000273491 <iSEEDESeq2Results>
    #> ENSG00000273492 <iSEEDESeq2Results>
    #> ENSG00000273493 <iSEEDESeq2Results>

    app <- iSEE(airway, initial = list(
      DETable(ContrastName="dex: trt vs untrt", HiddenColumns = c("baseMean",
        "lfcSE", "stat"), PanelWidth = 4L),
      VolcanoPlot(ContrastName="dex: trt vs untrt", PanelWidth = 4L),
      MAPlot(ContrastName="dex: trt vs untrt", PanelWidth = 4L)
    ))

    if (interactive()) {
        shiny::runApp(app)
    }

# 3 Reproducibility

The iSEEde package (Rue-Albrecht, 2024) was made possible thanks to:

- R (R Core Team, 2024)
- BiocStyle (Oleś, 2024)
- knitr (Xie, 2024)
- RefManageR (McLean, 2017)
- rmarkdown (Allaire, Xie, Dervieux et al., 2024)
- sessioninfo (Wickham, Chang, Flight et al., 2021)
- testthat (Wickham, 2011)

This package was developed using biocthis.

Code for creating the vignette

    ## Create the vignette
    library("rmarkdown")
    system.time(render("iSEEde.Rmd", "BiocStyle::html_document"))

    ## Extract the R code
    library("knitr")
    knit("iSEEde.Rmd", tangle = TRUE)

Date the vignette was generated.

    #> [1] "2024-10-29 20:32:05 EDT"

Wallclock time spent generating the vignette.

    #> Time difference of 22.454 secs

session information.

    #> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
    #>  setting  value
    #>  version  R version 4.4.1 (2024-06-14)
    #>  os       macOS Monterey 12.7.6
    #>  system   x86_64, darwin20
    #>  ui       X11
    #>  language (EN)
    #>  collate  C
    #>  ctype    en_US.UTF-8
    #>  tz       America/New_York
    #>  date     2024-10-29
    #>  pandoc   2.7.3 @ /usr/local/bin/ (via rmarkdown)
    #>
    #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
    #>  package              * version  date (UTC) lib source
    #>  abind                  1.4-8    2024-09-12 [2] CRAN (R 4.4.1)
    #>  airway               * 1.25.0   2024-05-02 [2] Bioconductor 3.20 (R 4.4.1)
    #>  AnnotationDbi        * 1.68.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  backports              1.5.0    2024-05-23 [2] CRAN (R 4.4.0)
    #>  beachmat               2.22.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  bibtex                 0.5.1    2023-01-26 [2] CRAN (R 4.4.0)
    #>  Biobase              * 2.66.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  BiocGenerics         * 0.52.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  BiocManager            1.30.25  2024-08-28 [2] CRAN (R 4.4.1)
    #>  BiocParallel           1.40.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  BiocStyle            * 2.34.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  Biostrings             2.74.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  bit                    4.5.0    2024-09-20 [2] CRAN (R 4.4.1)
    #>  bit64                  4.5.2    2024-09-22 [2] CRAN (R 4.4.1)
    #>  blob                   1.2.4    2023-03-17 [2] CRAN (R 4.4.0)
    #>  bookdown               0.41     2024-10-16 [2] CRAN (R 4.4.1)
    #>  bslib                  0.8.0    2024-07-29 [2] CRAN (R 4.4.0)
    #>  cachem                 1.1.0    2024-05-16 [2] CRAN (R 4.4.0)
    #>  circlize               0.4.16   2024-02-20 [2] CRAN (R 4.4.0)
    #>  cli                    3.6.3    2024-06-21 [2] CRAN (R 4.4.0)
    #>  clue                   0.3-65   2023-09-23 [2] CRAN (R 4.4.0)
    #>  cluster                2.1.6    2023-12-01 [2] CRAN (R 4.4.1)
    #>  codetools              0.2-20   2024-03-31 [2] CRAN (R 4.4.1)
    #>  colorspace             2.1-1    2024-07-26 [2] CRAN (R 4.4.1)
    #>  colourpicker           1.3.0    2023-08-21 [2] CRAN (R 4.4.0)
    #>  ComplexHeatmap         2.22.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  crayon                 1.5.3    2024-06-20 [2] CRAN (R 4.4.0)
    #>  DBI                    1.2.3    2024-06-02 [2] CRAN (R 4.4.0)
    #>  DelayedArray           0.32.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  DESeq2               * 1.46.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  digest                 0.6.37   2024-08-19 [2] CRAN (R 4.4.1)
    #>  doParallel             1.0.17   2022-02-07 [2] CRAN (R 4.4.0)
    #>  dplyr                  1.1.4    2023-11-17 [2] CRAN (R 4.4.0)
    #>  DT                     0.33     2024-04-04 [2] CRAN (R 4.4.0)
    #>  edgeR                * 4.4.0    2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  evaluate               1.0.1    2024-10-10 [2] CRAN (R 4.4.1)
    #>  fansi                  1.0.6    2023-12-08 [2] CRAN (R 4.4.0)
    #>  fastmap                1.2.0    2024-05-15 [2] CRAN (R 4.4.0)
    #>  fontawesome            0.5.2    2023-08-19 [2] CRAN (R 4.4.0)
    #>  foreach                1.5.2    2022-02-02 [2] CRAN (R 4.4.0)
    #>  generics               0.1.3    2022-07-05 [2] CRAN (R 4.4.0)
    #>  GenomeInfoDb         * 1.42.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  GenomeInfoDbData       1.2.13   2024-10-01 [2] Bioconductor
    #>  GenomicRanges        * 1.58.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  GetoptLong             1.0.5    2020-12-15 [2] CRAN (R 4.4.0)
    #>  ggplot2                3.5.1    2024-04-23 [2] CRAN (R 4.4.0)
    #>  ggrepel                0.9.6    2024-09-07 [2] CRAN (R 4.4.1)
    #>  GlobalOptions          0.1.2    2020-06-10 [2] CRAN (R 4.4.0)
    #>  glue                   1.8.0    2024-09-30 [2] CRAN (R 4.4.1)
    #>  gtable                 0.3.6    2024-10-25 [2] CRAN (R 4.4.1)
    #>  highr                  0.11     2024-05-26 [2] CRAN (R 4.4.0)
    #>  htmltools              0.5.8.1  2024-04-04 [2] CRAN (R 4.4.0)
    #>  htmlwidgets            1.6.4    2023-12-06 [2] CRAN (R 4.4.0)
    #>  httpuv                 1.6.15   2024-03-26 [2] CRAN (R 4.4.0)
    #>  httr                   1.4.7    2023-08-15 [2] CRAN (R 4.4.0)
    #>  igraph                 2.1.1    2024-10-19 [2] CRAN (R 4.4.1)
    #>  IRanges              * 2.40.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  iSEE                 * 2.18.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  iSEEde               * 1.4.0    2024-10-29 [1] Bioconductor 3.20 (R 4.4.1)
    #>  iterators              1.0.14   2022-02-05 [2] CRAN (R 4.4.0)
    #>  jquerylib              0.1.4    2021-04-26 [2] CRAN (R 4.4.0)
    #>  jsonlite               1.8.9    2024-09-20 [2] CRAN (R 4.4.1)
    #>  KEGGREST               1.46.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  knitr                  1.48     2024-07-07 [2] CRAN (R 4.4.1)
    #>  later                  1.3.2    2023-12-06 [2] CRAN (R 4.4.0)
    #>  lattice                0.22-6   2024-03-20 [2] CRAN (R 4.4.1)
    #>  lifecycle              1.0.4    2023-11-07 [2] CRAN (R 4.4.0)
    #>  limma                * 3.62.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  listviewer             4.0.0    2023-09-30 [2] CRAN (R 4.4.0)
    #>  locfit                 1.5-9.10 2024-06-24 [2] CRAN (R 4.4.0)
    #>  lubridate              1.9.3    2023-09-27 [2] CRAN (R 4.4.0)
    #>  magrittr               2.0.3    2022-03-30 [2] CRAN (R 4.4.0)
    #>  Matrix                 1.7-1    2024-10-18 [2] CRAN (R 4.4.1)
    #>  MatrixGenerics       * 1.18.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  matrixStats          * 1.4.1    2024-09-08 [2] CRAN (R 4.4.1)
    #>  memoise                2.0.1    2021-11-26 [2] CRAN (R 4.4.0)
    #>  mgcv                   1.9-1    2023-12-21 [2] CRAN (R 4.4.1)
    #>  mime                   0.12     2021-09-28 [2] CRAN (R 4.4.0)
    #>  miniUI                 0.1.1.1  2018-05-18 [2] CRAN (R 4.4.0)
    #>  munsell                0.5.1    2024-04-01 [2] CRAN (R 4.4.0)
    #>  nlme                   3.1-166  2024-08-14 [2] CRAN (R 4.4.1)
    #>  org.Hs.eg.db         * 3.20.0   2024-09-29 [2] Bioconductor
    #>  pillar                 1.9.0    2023-03-22 [2] CRAN (R 4.4.0)
    #>  pkgconfig              2.0.3    2019-09-22 [2] CRAN (R 4.4.0)
    #>  plyr                   1.8.9    2023-10-02 [2] CRAN (R 4.4.0)
    #>  png                    0.1-8    2022-11-29 [2] CRAN (R 4.4.0)
    #>  promises               1.3.0    2024-04-05 [2] CRAN (R 4.4.0)
    #>  R6                     2.5.1    2021-08-19 [2] CRAN (R 4.4.0)
    #>  RColorBrewer           1.1-3    2022-04-03 [2] CRAN (R 4.4.0)
    #>  Rcpp                   1.0.13   2024-07-17 [2] CRAN (R 4.4.1)
    #>  RefManageR           * 1.4.0    2022-09-30 [2] CRAN (R 4.4.0)
    #>  rintrojs               0.3.4    2024-01-11 [2] CRAN (R 4.4.0)
    #>  rjson                  0.2.23   2024-09-16 [2] CRAN (R 4.4.1)
    #>  rlang                  1.1.4    2024-06-04 [2] CRAN (R 4.4.0)
    #>  rmarkdown              2.28     2024-08-17 [2] CRAN (R 4.4.1)
    #>  RSQLite                2.3.7    2024-05-27 [2] CRAN (R 4.4.0)
    #>  S4Arrays               1.6.0    2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  S4Vectors            * 0.44.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  sass                   0.4.9    2024-03-15 [2] CRAN (R 4.4.0)
    #>  scales                 1.3.0    2023-11-28 [2] CRAN (R 4.4.0)
    #>  scuttle              * 1.16.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  sessioninfo          * 1.2.2    2021-12-06 [2] CRAN (R 4.4.0)
    #>  shape                  1.4.6.1  2024-02-23 [2] CRAN (R 4.4.0)
    #>  shiny                  1.9.1    2024-08-01 [2] CRAN (R 4.4.1)
    #>  shinyAce               0.4.3    2024-10-19 [2] CRAN (R 4.4.1)
    #>  shinydashboard         0.7.2    2021-09-30 [2] CRAN (R 4.4.0)
    #>  shinyjs                2.1.0    2021-12-23 [2] CRAN (R 4.4.0)
    #>  shinyWidgets           0.8.7    2024-09-23 [2] CRAN (R 4.4.1)
    #>  SingleCellExperiment * 1.28.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  SparseArray            1.6.0    2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  statmod                1.5.0    2023-01-06 [2] CRAN (R 4.4.0)
    #>  stringi                1.8.4    2024-05-06 [2] CRAN (R 4.4.0)
    #>  stringr                1.5.1    2023-11-14 [2] CRAN (R 4.4.0)
    #>  SummarizedExperiment * 1.36.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  tibble                 3.2.1    2023-03-20 [2] CRAN (R 4.4.0)
    #>  tidyselect             1.2.1    2024-03-11 [2] CRAN (R 4.4.0)
    #>  timechange             0.3.0    2024-01-18 [2] CRAN (R 4.4.0)
    #>  UCSC.utils             1.2.0    2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  utf8                   1.2.4    2023-10-22 [2] CRAN (R 4.4.0)
    #>  vctrs                  0.6.5    2023-12-01 [2] CRAN (R 4.4.0)
    #>  vipor                  0.4.7    2023-12-18 [2] CRAN (R 4.4.0)
    #>  viridisLite            0.4.2    2023-05-02 [2] CRAN (R 4.4.0)
    #>  xfun                   0.48     2024-10-03 [2] CRAN (R 4.4.1)
    #>  xml2                   1.3.6    2023-12-04 [2] CRAN (R 4.4.0)
    #>  xtable                 1.8-4    2019-04-21 [2] CRAN (R 4.4.0)
    #>  XVector                0.46.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>  yaml                   2.3.10   2024-07-26 [2] CRAN (R 4.4.1)
    #>  zlibbioc               1.52.0   2024-10-29 [2] Bioconductor 3.20 (R 4.4.1)
    #>
    #>  [1] /private/var/folders/db/4tvgx8jx4z3fm1gzlnlzw9rc0000gq/T/RtmpYZnTiw/Rinstdac52671b805
    #>  [2] /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library
    #>
    #> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

# 4 Bibliography

This vignette was generated using BiocStyle (Oleś, 2024) with knitr (Xie, 2024) and rmarkdown (Allaire, Xie, Dervieux et al., 2024) running behind the scenes.

Citations made with RefManageR (McLean, 2017).

[1] J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents for R. R package version 2.28. 2024. URL: https://github.com/rstudio/rmarkdown.

[2] M. W. McLean. “RefManageR: Import and Manage BibTeX and BibLaTeX References in R”. In: The Journal of Open Source Software (2017). DOI: 10.21105/joss.00338.

[3] A. Oleś. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.34.0. 2024. DOI: 10.18129/B9.bioc.BiocStyle. URL: https://bioconductor.org/packages/BiocStyle.

[4] R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria, 2024. URL: https://www.R-project.org/.

[5] K. Rue-Albrecht. iSEEde: iSEE extension for panels related to differential expression analysis. R package version 1.4.0. 2024. DOI: 10.18129/B9.bioc.iSEEde. URL: https://bioconductor.org/packages/iSEEde.

[6] H. Wickham. “testthat: Get Started with Testing”. In: The R Journal 3 (2011), pp. 5–10. URL: https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf.

[7] H. Wickham, W. Chang, R. Flight, et al. sessioninfo: R Session Information. R package version 1.2.2. 2021. URL: https://CRAN.R-project.org/package=sessioninfo.

[8] Y. Xie. knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.48. 2024. URL: https://yihui.org/knitr/.