This NEWS file mainly serves as a changelog file, i.e. a list of new features / bugfixes by version number. Versions uploaded to CRAN are marked with [CRAN]. Glossary: 'pr' means 'pull request' on GitHub 'issue' is an issue on GitHub The respective details can be found by visiting GitHub, e.g. https://github.com/cbielow/PTXQC/pull/124 for pr #124 (you can use the same URL also for issues, just change the number) ################################# ######### CHANGELOG ########## ################################# [CRAN] v1.1.1 -- 2024/03/11 - compatibility with latest ggplot2 (v. 3.5.0) (pr #135) [CRAN] v1.1.0 -- 2023/12/16 - new DDA metric: frequencies of variable modifications per Raw file (pr #134) [CRAN] v1.00.17 -- 2023/07/05 - support for the latest rmzqc package [CRAN] v1.00.17 -- 2023/07/05 - support for the latest rmzqc package (prepare for export) [CRAN] v1.00.16 -- 2023/05/17 - add MaxQuant 2.4 support (#130) [CRAN] v1.00.15 -- 2023/04/23 - better reporter ion minimum range in violin plot (pr #124) - workaround for MQ bug causing negative scan index in msms_scan.txt (issue #128) - use 'rmzqc' package to handle mzQC output (prepare for export) [CRAN] v1.00.14 -- 2022/09/21 - [FIX] crash when re-running PTX-QC on a txt folder where a (very old) PTX-QC was already run (issue #118) - [FIX] msmsScans TopNoverN metric showing invalid data for MaxQuant 2.x (issue #119) - [FEATURE] a better plot for TMT/iTRAQ reporter intensity (issue #123) - a few minor things (mainly CRAN docs) [CRAN] v1.00.13 -- 2022/03/22 - [FIX] Remove dependency 'kableExtra' and use 'htmlTable' package instead [CRAN] v1.00.12 -- 2021/11/02 - [FIX] Documentation and cosmetic fixes (pr #109) - [FIX/DOC] improved legends and better links in Html reports (pr #111) - [FIX] crash on Raw files with only a single MSMS spectrum (pr #112) [CRAN] v1.00.11 -- 2021/09/28 - [FEATURE] initial support for mzQC Quality Control output (pr #105) - [FEATURE] missed cleavages metric can be computed from evidence.txt now (pr #104) - [FIX] MSMSScans metric will crash on exotic data (pr #107) [CRAN] v1.0.10 -- 2021/05/29 - [FEATURE] detect if MaxQuant was run with wrong decimal separator (non UK/US locale) (issue #98) - [FIX] issue #97 Revive missing MBR metrics (introduced in PTXQC 1.0.9) - [FIX] issue #101 Restore full Parameter list showing MaxQuant parameters - [FIX] issue #102 Decoy distribution not shown in MS/MS mass error plot [CRAN] v1.0.9 -- 2021/01/29 - [FEATURE] allow redirecting console output to file (#94) - [FIX] reduce ggplot warnings - [FEATURE] mzQC data type support (preliminary; no export yet) [CRAN] v1.0.8 -- 2020/12/11 - [FIX] issue #90 Missed Cleavages Plot missing - [FIX] issue #91 Wrong score for MSMSScans Intensity [CRAN] v1.0.7 -- 2020/11/11 - [FIX] issue #82 cannot open file Rplots.pdf [CRAN] v1.0.6 -- 2020/09/09 - [FIX] issue #85 MzTabReader broken (again) [CRAN] v1.0.5 -- 2020/06/08 - [FIX] issue #81 MzTabReader broken - [FEATURE] remove redundant parameters (#78) [CRAN] v1.0.4 -- 2020/03/27 - [FIX] issue #78 duplicate characters in Parameters table - [FEATURE] support for labeled data from mzTab (requires OpenMS develop (pre 2.6)) v1.0.3 -- 2020/03/16 - [FIX] issue #54 create Html report without internet connection - [FIX] mzTab input: fix equal number of peptides/proteins for all Raw files (excessive transferred IDs estimate) - minor fixes for compatibility with R 4.0.0 (develop) [CRAN] v1.0.2 -- 2020/02/11 - minor fixes for CRAN compatibility [CRAN] v1.0.0 -- 2020/01/08 - [FEATURE] support for mzTab input data (e.g. from OpenMS 2.5 'QualityControl' tool) - [FEATURE] new metric: UpSetR plots (shows common sets of peptides across Raw files) - [FEATURE] new metric: Total Ion Count (TIC) plots (for OpenMS' mzTab input only; not supported for MaxQuant) - [FIX] issue #55 (MS2 Calibration metric crash when no evidence is given) - [FIX] issue #56 package data.table not properly imported [CRAN] v0.92.6 -- 2019/03/14 - [FIX] issue #51 (crash on MSMSScans) - [FIX] issue #54 (timsTOF data fix) [CRAN] v0.92.5 -- 2019/03/14 - [FIX] issue #49 (Raw name simplification) [CRAN] v0.92.4 -- 2019/02/07 - [FIX] More robust package vignette builds [CRAN] v0.92.3 -- 2018/02/06 - [FEATURE] List of Metrics (PTXQC_list-of-metrics.html) added v0.92.2 -- 2018/01/29 - [FEATURE] added plots and metrics of reporter intensity (iTRAQ, TMT, ...) for labeled MSn experiments v0.92.1 -- 2017/10/18 - [FIX] issue #41 (partial data problem) - [FIX] read/write report problem on Shiny.io [CRAN] v0.92.0 -- 2017/10/12 - [FIX] fix an issue where PTXQC would fail when drawing boxPlots (usually for large experiments only) - [FEATURE] - cleaner R interface to main report function (allowing to specify custom output files as arguments) - a log file is generated when using drag'n'drop; [CRAN] v0.91.0 -- 2017/10/06 - [DOC] Extended 'charge' plot html-documentation (linking to Bittremieux 2017, DOI: 10.1002/mas.21544). - [FIX] issue #39 (order of barchart items corrected after changes to ggplot package) issue #40 (custom contaminant plot error when not all Raw files are affected) [CRAN] v0.90.0 -- 2017/08/03 - [FEATURE] Tables are shown as genuine HTML tables in Html-Output [CRAN] v0.82.6 -- 2017/06/09 - [FIX] Special Contaminants searched by name in protein ID as well (issue #34) [CRAN] v0.82.5 -- 2017/05/04 - [FIX] More robust installation instructions for GitHub package (issue #32) v0.82.4 -- 2017/04/24 - [FIX] MS/MS fragment intensity plot fixed for MaxQuant 1.2 results (Basepeak Intensity column was renamed, issue #32) [CRAN] v0.82.3 -- 2017/04/03 - [FIX] MS/MS fragment plots can deal with 'Unknown' mass analyzer (e.g. from mzXML input) - [FIX] .yaml config file is written completely before actual analysis starts [CRAN] v0.82.2 -- 2017/02/18 - [FIX] fix Match-between-runs plotting when data is extremely sparse (issue #30) - [DOC] improved description of how to customize YAML config - [FEATURE] write out preliminary YAML config upon first invocation, enabling the user to disable metrics on failing runs v0.82.1 -- 2016/11/03 - fixes to new Dependent Peptides (DP) plot (issue #28) (added target sites in percent) v0.82.0 -- 2016/11/01 - [METRIC] new Dependent Peptides (DP) plot (issue #28) (if DP were enabled in MaxQuant, the Top5 modifications will be displayed; this allows to compare samples, but also hints at overlooked variable modifications) v0.81.0 -- 2016/10/18 - [METRIC] new experimental MS/MS intensity metric (scoring the MS/MS TIC vs. base peak, to look for bad ion transmission or fragmentation) [CRAN] v0.80.14 -- 2016/10/13 - CRAN test fix (make PANDOC optional -- prevents Html reports and Vignettes) [CRAN] v0.80.13 -- 2016/10/07 - minor documentation changes prior to CRAN submission v0.80.12 -- 2016/09/28 - bug fixes - fix error during in 'PG: Ratio Density' plot when all ratio data is empty (e.g. for blank samples) v0.80.11 -- 2016/08/11 - bug fixes - augment fix from v0.80.9 since MaxQuant for finding a MBR reference Raw file v0.80.10 -- 2016/08/04 - automatic detection which txt files are present [only these are used] v0.80.9 -- 2016/08/02 - bug fixes - MBR-Metric: if more than one RT-reference is found (which can happen for a VERY stable LC), the first is picked https://github.com/cbielow/PTXQC/issues/25 - minor doc improvements v0.80.8 -- 2016/07/13 - bug fixes - avoid crash in pre-calibration metric when there is only a single peptide identified in (any) Raw file v0.80.7 -- 2016/06/09 - features - support for 32bit R for Drag'n'Drop batch file - bug fixes - fix missing score distribution plots for custom contaminants - small documentation improvements v0.80.6 -- 2016/06/06 - bug fixes - fix NA's (empty bars) in MBR ID transfer plot for very sparse Raw files - fix crash when plotting EVD aux-plots for Raw files with NO ID's (0% id rate) v0.80.5 -- 2016/04/15 - bug fixes https://github.com/cbielow/PTXQC/issues/23 (EVD: MS/MS Oversampling bug) v0.80.4 -- 2016/04/11 - bug fixes https://github.com/cbielow/PTXQC/issues/22 (Drag'n'drop of folders with space character) v0.80.3 -- 2016/04/08 - bug fixes https://github.com/cbielow/PTXQC/issues/21 - Html report will be created prior to PDF file (if both are requested [default]) - minor doc improvments (Metric help texts in Html report) v0.80.2 -- 2016/04/04 - reduce memory footprint (~50% reduction; replacing ddply() with data.table[]) v0.80.1 -- 2016/03/15 - experimental missing value metric (on peptide level) - density plots (showing what intensities are usually missing) - includes simple inter-Raw file normalization scheme - percentage of missing values (lower is better) -- used for scoring in heatmap v0.80.0 -- 2016/02 - Report format is by default now Html and PDF (you get two identical reports) - Html report includes help texts describing each metric and scoring - order of metrics is now matching the wet-lab workflow (roughly), but can be customized (i.e. user-defined) using the YAML config - removed Bioconductor dependency (for easier installation) - bugfixes / minor improvements v0.70.3 - internal restructuring v0.70.2 - faster loading of txt files / better consistency checking - support for Chinese "NA" entries in Txt files v0.70.1 - fix empty parameter page (bug in 0.70.0) v0.70.0 - support for data containing MS3 scans