NEWS
PTXQC 1.0.3
- [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
PTXQC 0.92.2
- [FEATURE] added plots and metrics of reporter intensity (iTRAQ, TMT, ...) for labeled MSn experiments
PTXQC 0.92.1
- [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)
PTXQC 0.82.4
- [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
PTXQC 0.82.1
- fixes to new Dependent Peptides (DP) plot (issue #28) (added target sites in percent)
PTXQC 0.82.0
- [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)
PTXQC 0.81.0
- [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
PTXQC 0.80.12
- bug fixes
- fix error during in 'PG: Ratio Density' plot when all ratio data is empty (e.g. for blank samples)
PTXQC 0.80.11
- bug fixes
- augment fix from v0.80.9 since MaxQuant for finding a MBR reference Raw file
PTXQC 0.80.10
- automatic detection which txt files are present [only these are used]
PTXQC 0.80.9
- 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
PTXQC 0.80.8
- bug fixes
- avoid crash in pre-calibration metric when there is only a single peptide identified in (any) Raw file
PTXQC 0.80.7
- features
- support for 32bit R for Drag'n'Drop batch file
- bug fixes
- fix missing score distribution plots for custom contaminants
- small documentation improvements
PTXQC 0.80.6
- 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)
PTXQC 0.80.5
- bug fixes
https://github.com/cbielow/PTXQC/issues/23 (EVD: MS/MS Oversampling bug)
PTXQC 0.80.4
- bug fixes
https://github.com/cbielow/PTXQC/issues/22 (Drag'n'drop of folders with space character)
PTXQC 0.80.3
- 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)
PTXQC 0.80.2
- reduce memory footprint (~50% reduction; replacing ddply() with data.table[])
PTXQC 0.80.1
- 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
PTXQC 0.80.0
- 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
PTXQC 0.70.3
PTXQC 0.70.2
- faster loading of txt files / better consistency checking
- support for Chinese "NA" entries in Txt files
PTXQC 0.70.1
- fix empty parameter page (bug in 0.70.0)
PTXQC 0.70.0
- support for data containing MS3 scans