-
Groups of indistinguishable/ambiguous proteins can be captured in mzIdentML in "ProteinAmbiguityGroup" elements. Internally in OpenMS, they can be stored in `ProteinIdentification::indistinguishable_p…
-
We have a set of [warnings](http://bioconductor.org/checkResults/release/bioc-LATEST/mzR/) on all platforms in both release and devel:
```
* checking whether package ‘mzR’ can be installed ... WAR…
-
We recently are trying to reproduce the results of a published study with TMT-10. We used MSFraggerAdapter, followed by Percolator to calculate PEP, and ProteinProphet to do protein grouping. If we ta…
-
As noted by Chris Barnett in https://help.galaxyproject.org/t/duplicate-tools-and-datatypes/1694
EU has several datatypes that are presented for selection multiple times. The one he gathered are:
- …
-
Recent Galaxy versions support a [_citations_ tag](https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?highlight=%28citations%29#A.3Ccitations.3E_tag_set). This issue will track to process of …
-
I am wondering on how to analyze the mzid output from the MS-GF+ for protein quantifications. Which software of tools can be used to quantify proteins identified by this pipeline? I am stuck and I am …
-
When I convert a single file prot.xml file using idconvert, here's what I get:
[AminoAcid::Info] Invalid amino acid symbol:
Error processing file
-
I am wondering how can i add something like [Pseudomonas aeruginosa ](https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa#:~:text=Pseudomonas%20aeruginosa%20is%20a%20common,of%20considerable%20medica…
-
What scripts are these?
pepxml2csv -IPROPHET -header -cP=%s -OUT=%s %s &&
protxml2spectralcount -CSV=%s -OUT=%s %s &&
protxml2modifications -CSV=%s -OUT=%s %s &&
protxml2openb…
-
Hi,
I am experiencing an internal compiler error when trying to install the mzR package on my system (ubuntu 22.04 in WSL, R 4.3.2). The issue occurs regardless of whether I use GCC versions 9, 10 o…