Package: isoorbi 1.5.3

Caj Neubauer

isoorbi: Process Orbitrap Isotopocule Data

Read and process isotopocule data from an Orbitrap Isotope Solutions mass spectrometer. Citation: Kantnerova et al. (Nature Protocols, 2024).

Authors:Caj Neubauer [aut, cre, cph], Sebastian Kopf [aut], Kristýna Kantnerová [aut]

isoorbi_1.5.3.tar.gz
isoorbi_1.5.3.zip(r-4.7)isoorbi_1.5.3.zip(r-4.6)isoorbi_1.5.3.zip(r-4.5)
isoorbi_1.5.3.tgz(r-4.6-any)isoorbi_1.5.3.tgz(r-4.5-any)
isoorbi_1.5.3.tar.gz(r-4.7-any)isoorbi_1.5.3.tar.gz(r-4.6-any)
isoorbi_1.5.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
isoorbi/json (API)
NEWS

# Install 'isoorbi' in R:
install.packages('isoorbi', repos = c('https://isoverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/isoverse/isoorbi/issues

Pkgdown/docs site:https://isoorbi.isoverse.org

On CRAN:

Conda:

6.86 score 10 stars 23 scripts 250 downloads 51 exports 52 dependencies

Last updated from:786918476e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK221
source / vignettesOK323
linux-release-x86_64OK212
macos-release-arm64OK257
macos-oldrel-arm64OK258
windows-develOK218
windows-releaseOK157
windows-oldrelOK258
wasm-releaseOK139

Exports:orbi_add_blocks_to_plotorbi_add_to_aggregatororbi_adjust_blockorbi_aggregate_raworbi_analyze_shot_noiseorbi_calculate_ionsorbi_calculate_ratiosorbi_calculate_summarized_ratioorbi_check_isoraworbi_default_themeorbi_define_basepeakorbi_define_block_for_flow_injectionorbi_define_blocks_for_dual_inletorbi_export_data_to_excelorbi_filter_filesorbi_filter_flagged_dataorbi_filter_isotopoculesorbi_filter_isoxorbi_filter_satellite_peaksorbi_filter_scan_intensityorbi_filter_weak_isotopoculesorbi_find_isoxorbi_find_raworbi_flag_outliersorbi_flag_satellite_peaksorbi_flag_weak_isotopoculesorbi_get_aggregatororbi_get_blocks_infoorbi_get_dataorbi_get_example_filesorbi_get_isotopocule_coverageorbi_get_optionorbi_get_optionsorbi_get_problemsorbi_get_settingsorbi_identify_isotopoculesorbi_optionsorbi_plot_isotopocule_coverageorbi_plot_raw_dataorbi_plot_satellite_peaksorbi_plot_shot_noiseorbi_plot_spectraorbi_read_isoxorbi_read_raworbi_register_aggregatororbi_segment_blocksorbi_set_settingsorbi_show_problemsorbi_simplify_isoxorbi_start_aggregatororbi_summarize_results

Dependencies:arrowassertthatbitbit64cellrangerclicliprcpp11crayondplyrevaluatefarvergenericsggplot2gluegtablehighrhmsisobandknitrlabelinglifecyclemagrittropenxlsxpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppreadrreadxlrematchrlangS7scalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxfunyamlzip

Dual Inlet

Rendered fromdual_inlet.Rmdusingknitr::rmarkdownon May 18 2026.

Last update: 2025-10-03
Started: 2023-05-06

Flow Injection

Rendered fromflow_injection.Rmdusingknitr::rmarkdownon May 18 2026.

Last update: 2025-10-03
Started: 2023-11-08

Functionality Guide

Rendered fromfunctionality_guide.Rmdusingknitr::rmarkdownon May 18 2026.

Last update: 2025-10-04
Started: 2025-10-01

Readme and manuals

Help Manual

Help pageTopics
isoorbi: Process Orbitrap Isotopocule Dataisoorbi-package isoorbi
Plot blocks backgroundorbi_add_blocks_to_plot
Manually adjust block delimitersorbi_adjust_block
Aggregate data from raw filesorbi_aggregate_raw
Shot noise calculationorbi_analyze_shot_noise
Calculate ions from intensitiesorbi_calculate_ions
Calculate direct isotopocule ratiosorbi_calculate_ratios
Calculate isotopocule ratioorbi_calculate_summarized_ratio
Check for the isoorbi raw file readerorbi_check_isoraw
Default isoorbi plotting themeorbi_default_theme
Define the denominator for ratio calculationorbi_define_basepeak
Define data block for flow injectionorbi_define_block_for_flow_injection
Binning raw data into blocks for dual inlet analysesorbi_define_blocks_for_dual_inlet
Export data to excelorbi_export_data_to_excel
Basic generic data files filterorbi_filter_files
Filter out flagged dataorbi_filter_flagged_data
Filter isotopoculesorbi_filter_isotopocules
Filter isox filesorbi_filter_isox
Function replaced by 'orbi_flag_satellite_peaks()'orbi_filter_satellite_peaks
Function replaced by 'orbi_flag_outliers()'orbi_filter_scan_intensity
Function replaced by 'orbi_flag_weak_isotopocules()'orbi_filter_weak_isotopocules
Find isox filesorbi_find_isox
Find raw filesorbi_find_raw
Flag outlier scansorbi_flag_outliers
Flag minor satellite peaks Flags minor signals for an isotopocule that matches multiple peaks within its exact mass +/- tolerance interval in the same scan. These are often small satellite peaks generated by the Fourier transform. However, if there are satelite peaks of high intensity or very many satellite peaks, it can indicate that the m/z and tolerance setting used for identifying isotopcules need to be revisited. Visualize the flagged satellite peaks with 'orbi_plot_satellite_peaks()'.orbi_flag_satellite_peaks
Flag weak isotopoculesorbi_flag_weak_isotopocules
Summarize blocks infoorbi_get_blocks_info
Get data frame from aggregated dataorbi_get_data
Get available example file(s)orbi_get_example_files
Retrieve parsing problemsorbi_get_problems orbi_show_problems
Get all isoorbi package settingsorbi_get_settings
Identify isotopoculesorbi_identify_isotopocules
Package optionsget_pkg_options orbi_get_option orbi_get_options orbi_options
Isotopocule coverageorbi_get_isotopocule_coverage orbi_plot_isotopocule_coverage
Visualize dataorbi_plot_raw_data
Visualize satellite peaksorbi_plot_satellite_peaks
Make a shot noise plotorbi_plot_shot_noise
Plot mass spectraorbi_plot_spectra
Read IsoX fileorbi_read_isox
Read RAW filesorbi_read_raw
Segment data blocksorbi_segment_blocks
Set package settingsorbi_set_settings
Simplify IsoX dataorbi_simplify_isox
Dynamic data agreggatororbi_add_to_aggregator orbi_get_aggregator orbi_register_aggregator orbi_start_aggregator
Generate the results tableorbi_summarize_results