Giters
biodavidjm
/
artMS
Analytical R Tools for Mass Spectrometry
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Stargazers:
14
Watchers:
5
Issues:
189
Forks:
7
biodavidjm/artMS Issues
Update documentation: Run & technical replicates
Closed
4 years ago
Error in Protein ID overlap matrix from QC-ID-Overlap.pdf
Closed
3 years ago
Comments count
2
analysis of Quantification: add more options to remove outliers of abundance data: IQR, STD, keep
Closed
4 years ago
Fix artms_checkRawFileColumnName affecting artmsQualityControlSummaryExtended()
Closed
4 years ago
Update documentation
Closed
4 years ago
Change default name for artmsAnalysisQuantifications
Closed
4 years ago
Error in .artms_checkRawFileColumnName(x)
Closed
4 years ago
Comments count
7
Error reported when converting the data to MSStats format
Closed
4 years ago
Comments count
3
Add QCplots and ConditionPlot
Closed
3 years ago
Add error if not all the RawFiles in keys file are found in the evidence file
Closed
4 years ago
artmsProtein2SiteConversion error when processing UB data
Closed
4 years ago
artmsProtein2SiteConversion: deal with full uniprot id and stop if it doesn't
Closed
4 years ago
Update documentation
Closed
4 years ago
Replace reshape2 by data.table
Closed
4 years ago
Address Warning messages
Closed
4 years ago
Add %ni% as part of the main function library
Closed
5 years ago
artmsChangeColumnName add warning if "old" colname is not there
Closed
4 years ago
Acetyalation analysis
Closed
4 years ago
Analysis of quantifications imputation error
Closed
4 years ago
Fix analysis of Quantifications: add tryCatches to deal with accessing gprofiler
Closed
5 years ago
Require R > 3.6
Closed
4 years ago
Move case studies away from createData to a new script
Closed
4 years ago
Check that the columns are not all NULL
Closed
4 years ago
Analysis of quantification error: "Aggregation function missing: defaulting to length"
Closed
4 years ago
Comments count
1
Add check point on "modified sequence"
Closed
3 years ago
Prevent artmsWriteConfigYamlFile for overwriting existing config file
Closed
3 years ago
define global varialbles within each function
Closed
3 years ago
QC Plot MZ
Updated
5 years ago
Vignette: Add details of how to run analysis of quantification on PTMSITES
Closed
4 years ago
Remove outliers before boxplot of abundance values
Closed
4 years ago
Silac type of analysis 'breaks' are not unique error
Closed
5 years ago
Comments count
6
QC basic evidence-based: add controls and plots for technical replicates
Closed
4 years ago
Adjust the size of pdf generated by QC evidence extended function
Closed
4 years ago
Add density plots
Updated
4 years ago
Fix: add fix for PH in basic quality control function
Closed
4 years ago
add new function to calculate error bars (for plots)
Closed
4 years ago
Fraction of imputed values is zero in results.imputation.pdf
Updated
3 years ago
Comments count
3
artmsProtein2SiteConversion {artMS} error in everything
Closed
4 years ago
Comments count
1
QC: add missing values function
Updated
5 years ago
Error running qc Summary based
Closed
4 years ago
Error in x[["Version"]] : subscript out of bounds
Closed
4 years ago
Comments count
1
Add option to remove protein groups in evidence to saint and saintexpress
Updated
5 years ago
artmsAnalysisQuantification: add check point if modified sites/peptides analysis for enrichment
Closed
4 years ago
QC fails with 1 bioreplicate
Closed
4 years ago
Clean full uniprot id (sp|Entry|Entry_name)
Closed
4 years ago
Include RefSeq to convert sites
Closed
5 years ago
artmsFilterEvidenceContaminants only takes data frames as input
Updated
5 years ago
Include "leading razor protein" selection as part of filtering
Closed
5 years ago
Bug: artmsQualityControlEvidenceExtended fails with old maxquant versions
Closed
5 years ago
fix and update artmsProtein2SiteConversion
Closed
4 years ago
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