Package: flowTraceR 0.1.0
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:
flowTraceR_0.1.0.tar.gz
flowTraceR_0.1.0.zip(r-4.5)flowTraceR_0.1.0.zip(r-4.4)flowTraceR_0.1.0.zip(r-4.3)
flowTraceR_0.1.0.tgz(r-4.4-any)flowTraceR_0.1.0.tgz(r-4.3-any)
flowTraceR_0.1.0.tar.gz(r-4.5-noble)flowTraceR_0.1.0.tar.gz(r-4.4-noble)
flowTraceR_0.1.0.tgz(r-4.4-emscripten)flowTraceR_0.1.0.tgz(r-4.3-emscripten)
flowTraceR.pdf |flowTraceR.html✨
flowTraceR/json (API)
NEWS
| # 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
Last updated 2 years agofrom:9eb96116d9. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 09 2024 |
| R-4.5-win | OK | Nov 09 2024 |
| R-4.5-linux | OK | Nov 09 2024 |
| R-4.4-win | OK | Nov 09 2024 |
| R-4.4-mac | OK | Nov 09 2024 |
| R-4.3-win | OK | Nov 09 2024 |
| R-4.3-mac | OK | Nov 09 2024 |
Exports:analyze_connected_levelsanalyze_unknown_modsconnect_traceR_levelsconvert_all_levelsconvert_modified_peptidesconvert_precursorconvert_proteingroupsget_exampleget_unknown_modstrace_all_levelstrace_leveltrace_unique_common_pg
Dependencies:clicolorspacecomprehenrcpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Example Retention Time Distribution
Rendered fromExample_RT_distribution.Rmdusingknitr::rmarkdownon Nov 09 2024.Last update: 2022-06-01
Started: 2022-05-31
Requirements
Rendered fromRequirements.Rmdusingknitr::rmarkdownon Nov 09 2024.Last update: 2022-06-02
Started: 2022-05-31
Workflow
Rendered fromWorkflow.Rmdusingknitr::rmarkdownon Nov 09 2024.Last update: 2022-06-23
Started: 2022-05-31
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analysis of connected levels | analyze_connected_levels |
| Analysis of unknown modifications | analyze_unknown_mods |
| Connects traced levels | connect_traceR_levels |
| Conversion of software specific levels | convert_all_levels |
| Conversion of software specific modified peptide entries | convert_modified_peptides |
| Conversion of software specific precursor entries | convert_precursor |
| Conversion of software specific proteinGroups | convert_proteingroups |
| flowTraceR: a package for standardization of level information and tracking inter-software differences in bottom-up label-free proteomics | flowTraceR-package flowTraceR |
| Create example data | get_example |
| Check of converted modifications | get_unknown_mods |
| Trace common and unique identifications between different software outputs for all levels | trace_all_levels |
| Trace common and unique identifications between different software outputs | trace_level |
| Trace unique_common categorization for proteinGroup level | trace_unique_common_pg |