Merge branch 'main' of github.com:HUPO-PSI/mzQC

docs/pages/resource-guide.md

@@ -21,6 +21,50 @@ Metrics generating software with mzQC support:
 - [OpenMS](https://github.com/OpenMS/OpenMS): Open-source software C++ library for LC/MS data management and analyses.
 - [QCCalculator](https://github.com/bigbio/qccalculator): Python tool for base QC metric calculation from mzML, mzIdentML, and MaxQuant input files.
 - [Yamato / SwaMe / Prognosticator](https://github.com/PaulBrack/Yamato): SWATH-MS QC metrics generation tools.
+- [MsQuality](https://bioconductor.org/packages/release/bioc/html/MsQuality.html): An R Bioconductor package, which provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics. It supports the calculation of the following metrics.
+  - chromatography duration (MS:4000053)
+  - TIC quarters RT fraction (MS:4000054)
+  - MS1 quarter RT fraction (MS:4000055)
+  - MS2 quarter RT fraction (MS:4000056)
+  - MS1 TIC-change quartile ratios (MS:4000057)
+  - MS1 TIC quartile ratios (MS:4000058)
+  - number of MS1 spectra MS:4000059)
+  - number of MS2 spectra (MS:4000060)
+  - m/z acquisition range (MS:4000069)
+  - retention time acquisition range (MS:4000070)
+  - MS1 signal jump (10x) count (MS:4000097)
+  - MS1 signal fall (10x) count (MS:4000098)
+  - number of empty MS1 scans (MS:4000099)
+  - number of empty MS2 scans (MS:4000100)
+  - number of empty MS3 scans (MS:4000101)
+  - MS2 precursor intensity distribution Q1, Q2, Q3 (MS:4000116)
+  - MS2 precursor intensity distribution mean (MS:4000117)
+  - MS2 precursor intensity distribution sigma (MS:4000118)
+  - MS2 precursor median m/z of identified quantification data points (MS:4000152)
+  - interquartile RT period for identified quantification data points (MS:4000153)
+  - rate of the interquartile RT period for identified quantification data points (MS:4000154)
+  - area under TIC (MS:4000155)
+  - area under TIC RT quantiles (MS:4000156)
+  - extent of identified MS2 precursor intensity (MS:4000157)
+  - median of TIC values in the RT range in which the middle half of quantification data points are identified (MS:4000158)
+  - median of TIC values in the shortest RT range in which half of the quantification data points are identified (MS:4000159)
+  - MS2 precursor intensity range (MS:4000160)
+  - identified MS2 precursor intensity distribution Q1, Q2, Q3 (MS:4000161)
+  - unidentified MS2 precursor intensity distribution Q1, Q2, Q3 (MS:4000162)
+  - identified MS2 precursor intensity distribution mean (MS:4000163)
+  - unidentified MS2 precursor intensity distribution mean (MS:4000164)
+  - identified MS2 precursor intensity distribution sigma (MS:4000165)
+  - unidentified MS2 precursor intensity distribution sigma (MS:4000166)
+  - ratio of 1+ over 2+ of all MS2 known precursor charges (MS:4000167)
+  - ratio of 1+ over 2+ of identified MS2 known precursor charges (MS:4000168)
+  - ratio of 3+ over 2+ of all MS2 known precursor charges (MS:4000169)
+  - ratio of 3+ over 2+ of identified MS2 known precursor charges (MS:4000170)
+  - ratio of 4+ over 2+ of all MS2 known precursor charges (MS:4000171)
+  - ratio of 4+ over 2+ of identified MS2 known precursor charges (MS:4000172)
+  - mean MS2 precursor charge in all spectra (MS:4000173)
+  - mean MS2 precursor charge in identified spectra (MS:4000174)
+  - median MS2 precursor charge in all spectra (MS:4000175)
+  - median MS2 precursor charge in identified spectra (MS:4000176)
 
 ### A Hub for QC
 If you are looking for a home to your QC software or library, check out [MS-Quality-Hub](https://github.com/MS-Quality-Hub). All the above libraries have their development home there and some other very useful repositories.

docs/pages/tutorials.md

@@ -7,13 +7,13 @@ permalink: /tutorials/
 We have a couple of tutorials and guides to offer, this page will lead you to them:
 
 ### with python
-* read mzQC: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MS-Quality-hub/pymzqc/blob/v1.0.0rc1/jupyter/colab/read_in_5_minutes.ipynb)
-* write mzQC: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MS-Quality-hub/pymzqc/blob/v1.0.0rc1/jupyter/colab/write_in_5_minutes.ipynb)
+* read mzQC: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MS-Quality-hub/pymzqc/blob/v1.0.0rc2/jupyter/colab/read_in_5_minutes.ipynb)
+* write mzQC: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MS-Quality-hub/pymzqc/blob/v1.0.0rc2/jupyter/colab/write_in_5_minutes.ipynb)
 * demo video
 <iframe width="560" height="315" src="https://www.youtube.com/embed/vZXJuPl2yGw" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 
 ### with R
-* [Rlib for mzQC(TBA)](TBA)
+* [rmzQC](https://cran.r-project.org/web/packages/rmzqc/index.html)
 * PTXQC demo
 <iframe width="560" height="315" src="https://www.youtube.com/embed/sb-mydbNRS4" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>