Changes in version 1.0.3 o [FIX] issue #54 create Html report without internet connection o [FIX] mzTab input: fix equal number of peptides/proteins for all Raw files (excessive transferred IDs estimate) o minor fixes for compatibility with R 4.0.0 (develop) [CRAN] v1.0.2 -- 2020/02/11 o minor fixes for CRAN compatibility [CRAN] v1.0.0 -- 2020/01/08 o [FEATURE] support for mzTab input data (e.g. from OpenMS 2.5 'QualityControl' tool) o [FEATURE] new metric: UpSetR plots (shows common sets of peptides across Raw files) o [FEATURE] new metric: Total Ion Count (TIC) plots (for OpenMS' mzTab input only; not supported for MaxQuant) o [FIX] issue #55 (MS2 Calibration metric crash when no evidence is given) o [FIX] issue #56 package data.table not properly imported [CRAN] v0.92.6 -- 2019/03/14 o [FIX] issue #51 (crash on MSMSScans) o [FIX] issue #54 (timsTOF data fix) [CRAN] v0.92.5 -- 2019/03/14 o [FIX] issue #49 (Raw name simplification) [CRAN] v0.92.4 -- 2019/02/07 o [FIX] More robust package vignette builds [CRAN] v0.92.3 -- 2018/02/06 o [FEATURE] List of Metrics (PTXQC_list-of-metrics.html) added Changes in version 0.92.2 o [FEATURE] added plots and metrics of reporter intensity (iTRAQ, TMT, ...) for labeled MSn experiments Changes in version 0.92.1 o [FIX] issue #41 (partial data problem) o [FIX] read/write report problem on Shiny.io [CRAN] v0.92.0 -- 2017/10/12 o [FIX] fix an issue where PTXQC would fail when drawing boxPlots (usually for large experiments only) o [FEATURE] - cleaner R interface to main report function (allowing to specify custom output files as arguments) o a log file is generated when using drag'n'drop; [CRAN] v0.91.0 -- 2017/10/06 o [DOC] Extended 'charge' plot html-documentation (linking to Bittremieux 2017, DOI: 10.1002/mas.21544). o [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 o [FEATURE] Tables are shown as genuine HTML tables in Html-Output [CRAN] v0.82.6 -- 2017/06/09 o [FIX] Special Contaminants searched by name in protein ID as well (issue #34) [CRAN] v0.82.5 -- 2017/05/04 o [FIX] More robust installation instructions for GitHub package (issue #32) Changes in version 0.82.4 o [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 o [FIX] MS/MS fragment plots can deal with 'Unknown' mass analyzer (e.g. from mzXML input) o [FIX] .yaml config file is written completely before actual analysis starts [CRAN] v0.82.2 -- 2017/02/18 o [FIX] fix Match-between-runs plotting when data is extremely sparse (issue #30) o [DOC] improved description of how to customize YAML config o [FEATURE] write out preliminary YAML config upon first invocation, enabling the user to disable metrics on failing runs Changes in version 0.82.1 o fixes to new Dependent Peptides (DP) plot (issue #28) (added target sites in percent) Changes in version 0.82.0 o [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) Changes in version 0.81.0 o [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 o CRAN test fix (make PANDOC optional -- prevents Html reports and Vignettes) [CRAN] v0.80.13 -- 2016/10/07 o minor documentation changes prior to CRAN submission Changes in version 0.80.12 o bug fixes o fix error during in 'PG: Ratio Density' plot when all ratio data is empty (e.g. for blank samples) Changes in version 0.80.11 o bug fixes o augment fix from v0.80.9 since MaxQuant for finding a MBR reference Raw file Changes in version 0.80.10 o automatic detection which txt files are present [only these are used] Changes in version 0.80.9 o bug fixes o 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 o minor doc improvements Changes in version 0.80.8 o bug fixes o avoid crash in pre-calibration metric when there is only a single peptide identified in (any) Raw file Changes in version 0.80.7 o features o support for 32bit R for Drag'n'Drop batch file o bug fixes o fix missing score distribution plots for custom contaminants o small documentation improvements Changes in version 0.80.6 o bug fixes o fix NA's (empty bars) in MBR ID transfer plot for very sparse Raw files o fix crash when plotting EVD aux-plots for Raw files with NO ID's (0% id rate) Changes in version 0.80.5 o bug fixes https://github.com/cbielow/PTXQC/issues/23 (EVD: MS/MS Oversampling bug) Changes in version 0.80.4 o bug fixes https://github.com/cbielow/PTXQC/issues/22 (Drag'n'drop of folders with space character) Changes in version 0.80.3 o bug fixes https://github.com/cbielow/PTXQC/issues/21 o Html report will be created prior to PDF file (if both are requested [default]) o minor doc improvments (Metric help texts in Html report) Changes in version 0.80.2 o reduce memory footprint (~50% reduction; replacing ddply() with data.table[]) Changes in version 0.80.1 o experimental missing value metric (on peptide level) o density plots (showing what intensities are usually missing) o includes simple inter-Raw file normalization scheme o percentage of missing values (lower is better) -- used for scoring in heatmap Changes in version 0.80.0 o Report format is by default now Html and PDF (you get two identical reports) o Html report includes help texts describing each metric and scoring o order of metrics is now matching the wet-lab workflow (roughly), but can be customized (i.e. user-defined) using the YAML config o removed Bioconductor dependency (for easier installation) o bugfixes / minor improvements Changes in version 0.70.3 o internal restructuring Changes in version 0.70.2 o faster loading of txt files / better consistency checking o support for Chinese "NA" entries in Txt files Changes in version 0.70.1 o fix empty parameter page (bug in 0.70.0) Changes in version 0.70.0 o support for data containing MS3 scans