PTXQC Versions Save

[CRAN] v1.1.1 -- 2024/03/11

• compatibility with latest ggplot2 (v. 3.5.0) (pr #135)

Full Changelog: https://github.com/cbielow/PTXQC/compare/v1.1.0...v1.1.1

[CRAN] v1.1.0 -- 2023/12/16

• new DDA metric: frequencies of variable modifications per Raw file (pr #134)

[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

• [FIX] crash when re-running PTX-QC on a txt folder where a (very old) PTX-QC was already run (issue https://github.com/cbielow/PTXQC/issues/118)
• [FIX] msmsScans TopNoverN metric showing invalid data for MaxQuant 2.x (issue https://github.com/cbielow/PTXQC/issues/119)
• [FEATURE] a better plot for TMT/iTRAQ reporter intensity (issue https://github.com/cbielow/PTXQC/issues/123)
• a few minor things (mainly CRAN docs)

remove kableExtra dependency package (see https://github.com/cbielow/PTXQC/pull/116)

• [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)

• initial support for mzQC Quality Control output (https://github.com/cbielow/PTXQC/pull/105)
• Missed cleavages can be computed from evidence.txt (https://github.com/cbielow/PTXQC/pull/104)
• minor fixes

[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

• [FEATURE] allow redirecting console output to file (#94)
• [FIX] reduce ggplot warnings
• [FEATURE] mzQC data type support (preliminary; no export yet)

fixes issues #90 (Missed Cleavage plot missing, since 1.0.5) and #91 (Wrong heatmap score for MSMSScans:Intensity, since beginning of time)