Title: Interactive Feature-Based Analysis of AIRR-Seq Data
Version: 1.0.0
Description: An interactive framework for the exploration and analysis of adaptive immune receptor repertoire sequencing (AIRR-seq) data. It enables large-scale computation and integrated analysis of sequence-derived features, including physicochemical properties, amino acid descriptor sets, sequence motifs, compositional patterns, and somatic hypermutation metrics. The application supports multiscale analysis across sequences, clones, and repertoires, with interactive visualizations and statistical feature selection. 'AbSolution' also facilitates reproducible research by enabling structured export of data, code, parameters, and computational environments. See https://github.com/EDS-Bioinformatics-Laboratory/AbSolution for more details.
License: GPL (≥ 3)
URL: https://github.com/EDS-Bioinformatics-Laboratory/AbSolution, https://eds-bioinformatics-laboratory.github.io/AbSolution/
BugReports: https://github.com/EDS-Bioinformatics-Laboratory/AbSolution/issues
Depends: R (≥ 4.4.0)
Imports: alakazam, attachment, benchmarkme, bigassertr, bigparallelr, bigstatsr, Biostrings, bs4Dash, callr, colourpicker, config (≥ 0.3.2), dashboardthemes, data.table, dockerfiler, doParallel, dplyr, DT, foreach, fresh, fs, ggplot2, golem (≥ 0.4.1), grDevices, htmlwidgets, IRanges, iterors, knitr, parallel, Peptides, plotly, pwalign, reactable, rlang, rmarkdown, seqinr, shiny (≥ 1.7.4), shinycssloaders, shinyFiles, shinyjs, shinymanager, shinymeta, shinythemes, shinyWidgets, sortable, stats, stringdist, stringr, sunburstR, tools, umap, upsetjs, utils, viridis, xfun
Suggests: testthat (≥ 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-04-17 09:32:04 UTC; rgarcia
Author: Rodrigo García-Valiente ORCID iD [cre, aut] (email2: rodrigo.garcia.valiente+absolution@email.com), Charisios Triantafyllou ORCID iD [aut], Antoine van Kampen ORCID iD [aut, ths]
Maintainer: Rodrigo García-Valiente <r.garciavaliente@amsterdamumc.nl>
Repository: CRAN
Date/Publication: 2026-04-21 19:22:25 UTC

Ab_palette: color ranges adapted to the BCR/TCR gene structure

Description

#' @description **Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead. Returns a vector of colors according to the input. For V/D/J/VJ/VDJ inputs, the colors are produced in a way that genes and combination of genes from the same family are assigned a similar color.

Usage

Ab_palette(
  list_values,
  vect_genes_comb = NA,
  type_values = c("V", "D", "J", "VJ", "VDJ", "cuantitative", "cualitative"),
  colorblind = FALSE,
  seed = 1234
)

Arguments

list_values

For V(D)J combinations, a list of lists of the families of each segment and the genes within them. For V/D/J segments, a list of the families and the genes within them. For cuantitative or cualitative values, a list of values.

vect_genes_comb

The vector of the V(D)J combinations present in the dataset if type_values is 'VJ' or 'VDJ'. Otherwise, NA.

type_values

One of 'V','D','J','VJ','VDJ', 'cuantitative' or 'cualitative'. 'V','D','J','VJ','VDJ',

colorblind

If TRUE, the output is a colorblind-friendly vector of colors from the viridis package. The similarity of the V-D-J colors is lost.

Value

palette_colors: a (named) vector of colors

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

2_Feature_determination_1

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead.

Usage

Feature_1(path_base, grouping_by)

Value

The return value, if any, from executing the function.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

2_Feature_determination_2

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead.

Usage

Feature__dataset(
  path_base,
  DF_to_parse,
  name_DF_to_parse,
  FWR1partial,
  FWR4partial,
  standard = TRUE
)

Value

The return value, if any, from executing the function.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

Big PCA

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead. A function to perform PCA over a FBM object.

Usage

big_PCA(FBM, rows, columns)

Arguments

FBM

A FBM object.

rows

Index of rows of the FBM that will be used to calculate the PCA.

columns

Index of columns of the FBM that will be used to calculate the PCA..

Value

A list with the PCA scores and its explained variances

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

4_Clonal_exploration

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead.

Usage

calculate_clone(
  seq_df,
  clonotype,
  AA_or_NT = "NT",
  region = "CDR3",
  percentage = 100,
  calculate_shared_clones
)

Value

The return value, if any, from executing the utility.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

5_Feature_exploration

Description

A utils function

Usage

draw_feature_violinplot(
  values,
  name_values,
  sequence_info_df,
  group_info,
  additional_group_info = "Patient",
  show_reconstructed,
  compare_opposites = FALSE,
  selected_rows,
  selected_subclones = NULL,
  selected_clones = NULL,
  hide_dots = FALSE,
  really_hide_dots = FALSE,
  width = 1400,
  height = 1000,
  img_type = "png",
  scale = 4,
  seed = 1234,
  source = "feature_violinplot",
  primary_color = "#09BC8A"
)

Value

The return value, if any, from executing the utility.

4_Clonal_exploration

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead.

Usage

draw_sharedclonesplot(
  seq_df,
  sets = NULL,
  group = "Patient",
  selected_rows,
  clonotype,
  AA_or_NT = "AA",
  region = "CDR3",
  percentage = 100,
  freq_filter = 0,
  Selected_clones = NULL,
  dominance_threshold,
  color_by = "Clonal sharing",
  colorblind,
  Big_mem_color_values,
  seed = 1234,
  width = 1400,
  height = 1000,
  img_type = "png",
  scale = 4
)

Value

The return value, if any, from executing the utility.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

4_Clonal_exploration

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead.

Usage

draw_upsetplot(
  seq_df,
  group = "Patient",
  selected_rows,
  clonotype,
  AA_or_NT = "AA",
  region = "CDR3",
  percentage = 100,
  freq_filter = 0,
  Selected_clones = NULL
)

Value

The return value, if any, from executing the utility.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

4_Clonal_exploration

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead.

Usage

draw_violinplots(
  seq_df,
  group = "Patient_Sample",
  selected_rows,
  clonotype,
  AA_or_NT = "AA",
  region = "CDR3",
  percentage = 100,
  freq_filter = 0,
  Selected_clones = NULL,
  dominance_threshold,
  seed = 1234,
  really_hide_dots = FALSE,
  width = 1400,
  height = 1000,
  img_type = "png",
  scale = 4,
  source = "clone_violinplot"
)

Value

The return value, if any, from executing the utility.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

3_Data_processing

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead.

Usage

filter_merged(
  FBM,
  merged_df,
  merged_header,
  use_rgermline,
  use_repertoire,
  use_productive,
  use_nonproductive,
  my_regions,
  my_var_elements,
  my_vars,
  my_vartypes,
  use_sharedVDJ,
  V_J_to_use,
  groups,
  group_A,
  group_B,
  group_C,
  univlog = FALSE,
  samples_to_keep,
  variables_to_remove,
  pval_type,
  pval_cutoff,
  estimate_cutoff,
  number_selected_vars,
  VJ_deselected,
  VDJ_normalized_per_size,
  R_mut_threshold_min,
  R_mut_threshold_max,
  to_compare_groups,
  VDJ_maximize_clones,
  VDJ_normalized_per_sample,
  my_clone_def,
  seed,
  chains,
  igsubtypes
)

Value

The return value, if any, from executing the function.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

Merge FBMs and meta files

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead. A function to join by row individual FBMs and .info files into a unique FBM and a unique .info file, merged_bm.

Usage

merge_FBMs(filepath)

Arguments

filepath

Path to the individual FBMs.

Value

A list with the merged FBM, the merged info file and the FBM header.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

1_Parsing

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead.

Usage

parse_AIRRSeq_file(
  file,
  group,
  patient,
  subgroup,
  sample,
  input_path,
  C_region_included,
  FWR1partial,
  FWR4partial,
  D_gene,
  repertoire,
  output_path,
  is_example = FALSE
)

Value

The return value, if any, from executing the function.

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.

Run the AbSolution Shiny Application Launches the interactive AbSolution Shiny application for exploring B-cell and T-cell receptor repertoire data. The application provides tools for loading AIRR-formatted datasets, inspecting sequence characteristics, visualizing clonotype distributions, and generating summary reports.

Description

Internally, 'run_app()' calls ['shiny::shinyApp()'] to start the application, using the UI defined in [app_ui()] and the server logic defined in [app_server()].

Usage

run_app(
  verbose = FALSE,
  onStart = NULL,
  options = list(),
  enableBookmarking = "server",
  uiPattern = "/",
  ...
)

Arguments

verbose

Logical. If FALSE (default), suppresses all warnings and messages during app execution. Set to TRUE to see full console output for debugging.

onStart

A function that will be called before the app is actually run. This is only needed for shinyAppObj, since in the shinyAppDir case, a global.R file can be used for this purpose.

options

Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.

enableBookmarking

Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See enableBookmarking() for more information on bookmarking your app.

uiPattern

A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.

...

arguments to pass to golem_opts. See '?golem::get_golem_options' for more details.

Details

This function is the entry point that end-users should call after installing the package.

Examples

if (interactive()) {
  ### Launch the full application with default settings:
  run_app()
}

Check parameters in 3. are properly selected

Description

**Internal function.** Not intended for direct use. Exported only for 'shinymeta' report rendering via '::' access. Use [run_app()] instead. A function to perform PCA over a FBM object.

Usage

validate_before_run(
  work_as_categories,
  use_sharedVDJ,
  VJ_included,
  VDJ_maximize_clones,
  clonal_group
)

Examples


  # Internal function exported for shinymeta :: access during report rendering.
  # Requires a live Shiny reactive context and real AIRR-seq data.
  # Use run_app() as the user-facing entry point.