Package: flowTraceR 0.1.1

Oliver Kardell

flowTraceR: Tracing Information Flow for Inter-Software Comparisons in Mass Spectrometry-Based Bottom-Up Proteomics

Useful functions to standardize software outputs from ProteomeDiscoverer, Spectronaut, DIA-NN and MaxQuant on precursor, modified peptide and proteingroup level and to trace software differences for identifications such as varying proteingroup denotations for common precursor.

Authors:Oliver Kardell [aut, cre]

flowTraceR_0.1.1.tar.gz
flowTraceR_0.1.1.zip(r-4.7-any)flowTraceR_0.1.1.zip(r-4.6-any)flowTraceR_0.1.1.zip(r-4.5-any)
flowTraceR_0.1.1.tgz(r-4.6-any)flowTraceR_0.1.1.tgz(r-4.5-any)
flowTraceR_0.1.1.tar.gz(r-4.7-any)flowTraceR_0.1.1.tar.gz(r-4.6-any)
flowTraceR_0.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowTraceR/json (API)

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

Bug tracker:https://github.com/okdll/flowtracer/issues

On CRAN:

Conda:

5.21 score 3 stars 1 packages 12 scripts 418 downloads 12 exports 30 dependencies

Last updated from:535be57b4a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK162
source / vignettesOK221
linux-releaseOK142
macos-releaseOK171
macos-oldrelOK160
windows-develOK89
windows-releaseOK95
windows-oldrelOK104
wasm-releaseOK128

Exports:analyze_connected_levelsanalyze_unknown_modsconnect_traceR_levelsconvert_all_levelsconvert_modified_peptidesconvert_precursorconvert_proteingroupsget_exampleget_unknown_modstrace_all_levelstrace_leveltrace_unique_common_pg

Dependencies:clicomprehenrcpp11dplyrfarvergenericsggplot2gluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrlangS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Workflow
Introduction | Loading R packages | Import | Import your data | Examples | Conversion to standardized format | Precursor | Modified Peptides | ProteinGroups | All Levels | Analyzing Conversion | Example precursor level | For each individual level | All levels | Connect traced levels | Show software differences for modified peptide/proteinGroup denotations | Example proteinGroup level | Get software difference for proteinGroup denotations | Results:
Rendered fromWorkflow.Rmdusingknitr::rmarkdown

Last update: 2022-06-23
Started: 2022-05-31

Requirements
Introduction | Spectronaut | MaxQuant | DIA-NN | Proteome Discoverer
Rendered fromRequirements.Rmdusingknitr::rmarkdown

Last update: 2022-06-02
Started: 2022-05-31

Example Retention Time Distribution
Introduction | Loading R packages | Preparation | Conversion to standardized format | RT distribution | Without flowTraceR | With flowTraceR | Inter-software comparison | Common entries | Unique entries
Rendered fromExample_RT_distribution.Rmdusingknitr::rmarkdown

Last update: 2022-06-01
Started: 2022-05-31