ComplexBrowser

ComplexBrowser is an R/Shiny application and R package for supervised proteomics analysis focused on protein complexes.

The original application is described in the manuscript: https://doi.org/10.1074/mcp.TIR119.001434

The current development version keeps the Shiny app, but also exposes reusable R functions and a small command-line interface for non-interactive workflows.

Current Entry Points

• Shiny app: inst/shiny/ui.R, inst/shiny/server.R, and inst/shiny/Global.R
• R package APIs: R/
• Shiny-only plotting helpers: inst/shiny/R/
• Shiny app assets, report template, and bundled example input: inst/shiny/
• Bundled prepared databases: inst/extdata/
• Reusable example input files for R/CLI workflows: inst/extdata/examples/
• Historical source data and old database snapshots: data-raw/legacy/
• Package workflow vignettes: vignettes/
• Command-line wrapper script: exec/complexbrowser
• OpenSpec behavior documents: openspec/specs/

Installation

From the repository root:

install.packages(".", repos = NULL, type = "source")

For development without installation:

pkgload::load_all(".")

The package name is lower-case:

library(complexbrowser)

Running the Shiny App

From the repository checkout:

shiny::runApp("inst/shiny")

After installing the package:

complexbrowser::complexbrowser_run_app()

Equivalent explicit form:

shiny::runApp(system.file("shiny", package = "complexbrowser"))

Docker

The Docker image installs the package, then serves the packaged Shiny app from system.file("shiny", package = "complexbrowser") through Shiny Server.

docker build -t complexbrowser .
docker run --rm -p 3838:3838 complexbrowser

The deployed app may also be available at: http://computproteomics.bmb.sdu.dk/Apps/ComplexBrowser

The historical tutorial is available here: https://bitbucket.org/michalakw/complexbrowser/raw/dcaef828f7f0f9501c4f041391471b94acf00be1/Manual.pdf

R Usage

QC/statistics

library(complexbrowser)

input <- read.csv("input.csv", check.names = FALSE)

qc <- complexbrowser_run_qc(
  data = input,
  no_cond = 2,
  no_rep = 4,
  grouped = TRUE,
  log2 = FALSE,
  q_values = FALSE,
  design = "unpaired"
)

head(qc$merged_table)

Complex Analysis

complex <- complexbrowser_run_complex_analysis(
  stats = qc$stats,
  database = "CORUM",
  organism = "Mus musculus",
  no_cond = 2,
  no_rep = 4,
  database_name = "CORUM"
)

head(complex$display_table)

Bundled databases can also be loaded explicitly:

corum <- complexbrowser_load_corum()
ebi <- complexbrowser_load_complex_portal()

Example files bundled with the installed package can be located with:

system.file("extdata", "examples", "myo.csv", package = "complexbrowser")
system.file("shiny", "data", "UserDB_EXAMPLE.csv", package = "complexbrowser")

Command-Line Usage

The CLI is intentionally thin: it parses arguments, reads input, calls the same package APIs used above, and writes CSV/RDS outputs. It does not launch Shiny and does not render plots or reports.

R packages do not normally install executables directly onto your shell PATH. The most portable way to run the CLI is through Rscript:

Rscript -e 'status <- complexbrowser::complexbrowser_cli(commandArgs(TRUE)); quit(save="no", status=as.integer(status), runLast=FALSE)' --args qc \
  --input input.csv \
  --outdir results \
  --conditions 2 \
  --replicates 4 \
  --grouped true \
  --log2 false \
  --q-values false

Complex analysis from the shell:

Rscript -e 'status <- complexbrowser::complexbrowser_cli(commandArgs(TRUE)); quit(save="no", status=as.integer(status), runLast=FALSE)' --args complex \
  --input input.csv \
  --outdir results \
  --conditions 2 \
  --replicates 4 \
  --grouped true \
  --log2 false \
  --q-values false \
  --database CORUM \
  --organism "Mus musculus"

The package also installs the helper script under its package directory. You can call it directly after installing the package:

"$(Rscript -e 'cat(system.file("exec", "complexbrowser", package="complexbrowser"))')" qc \
  --input input.csv \
  --outdir results \
  --conditions 2 \
  --replicates 4

For frequent use, create a local wrapper such as ~/bin/complexbrowser:

#!/usr/bin/env sh
exec Rscript -e 'status <- complexbrowser::complexbrowser_cli(commandArgs(TRUE)); quit(save="no", status=as.integer(status), runLast=FALSE)' --args "$@"

Then make it executable:

chmod +x ~/bin/complexbrowser

After that, assuming ~/bin is on your PATH:

complexbrowser qc --input input.csv --outdir results --conditions 2 --replicates 4

CLI Outputs

qc writes:

• input_statistics.csv
• qc_result.rds

complex writes:

• input_statistics.csv
• qc_result.rds
• complex_result.rds
• complex_table.csv when matching complexes are found

No matching complexes is treated as a successful analysis result. In that case complex_result.rds is written and complex_table.csv is omitted.

Input Notes

• The first input column must contain protein identifiers.
• Measurement columns must match the --conditions, --replicates, and --grouped settings.
• q-value columns may be supplied, or q-values can be calculated with LIMMA.
• Complex analysis supports CORUM, EBI Complex Portal, or a user-defined database CSV with the expected complex columns.

Validation

The current package has test coverage for:

• QC fixture parity
• complex-analysis fixture parity
• bundled database accessors
• CSV/RDS exports
• CLI QC and complex-analysis smoke tests
• Shiny smoke tests for core workflows

Typical local checks:

Rscript -e 'pkgload::load_all(".", quiet=TRUE); testthat::test_dir("tests/testthat", reporter="summary")'
R CMD build --no-build-vignettes .
R CMD check --no-manual --no-build-vignettes complexbrowser_*.tar.gz
openspec validate --specs --strict --no-interactive

Current Limitations

• The CLI covers tabular QC and complex-analysis outputs, not Shiny-only interactive plots.
• The QC PDF report remains part of the Shiny workflow.
• The shell convenience command requires either the installed package script path or a user-created wrapper.

Legacy Links

Historical released versions: https://bitbucket.org/michalakw/complexbrowser/downloads/?tab=tags

Historical source downloads: https://bitbucket.org/michalakw/complexbrowser/downloads/?tab=downloads