Giters
biodavidjm
/
artMS
Analytical R Tools for Mass Spectrometry
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Stargazers:
14
Watchers:
5
Issues:
189
Forks:
7
biodavidjm/artMS Issues
Question about filtering conditions with MSstats quantification
Updated
a year ago
Comments count
2
Could you please add MSStats removeFewMeasurements argument in the config.yaml?
Updated
a year ago
Feature request: allow duplications for artmsMapUniprot2Entrez
Updated
2 years ago
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'select': object 'org.Mm.eg.db' not found
Updated
2 years ago
Error: "supply both 'x' and 'y' or a matrix-like 'x'"
Closed
2 years ago
Comments count
3
Question about SILAC data analysis
Updated
2 years ago
Error: Assigned data `dfdc.final[[x]] - dfdc.final[[y]]` must be compatible with existing data
Updated
3 years ago
Comments count
11
Problem about user-defined modification type
Updated
3 years ago
Comments count
8
Error in vecseq(f__, len__, if (allow.cartesian || notjoin || !anyDuplicated
Closed
3 years ago
Comments count
15
question about user modification
Updated
3 years ago
Comments count
14
Would be great to support additional PTMs in a way that doesn't require recoding artMS for each new PTM
Closed
3 years ago
Add checkpoint to validate naming rules of the keys file
Updated
3 years ago
org.*.eg.db packages other than mouse/human are not in namespace
Updated
3 years ago
Comments count
1
Deprecate protein complex enrichment analysis
Updated
3 years ago
Replace gProfileR by gprofiler2
Updated
3 years ago
Remove negative values from ModelQC
Updated
3 years ago
New format of modifications from MaxQuant cause artmsProtein2SiteConversion to fail
Updated
3 years ago
Comments count
4
Fix: message of number of Intensity values = 0
Updated
3 years ago
Minor issue in artms_getMSstatsFormat default parameters, future bug maybe
Closed
3 years ago
Comments count
1
Add printPDF to analysis of Quantifications
Closed
3 years ago
Create folders
Closed
3 years ago
Issue with results-summary.xlsx (in "wide" tables, missing results get iLog2FC and iPvalue = 0)
Closed
3 years ago
Comments count
2
MSstats changes
Closed
3 years ago
Comments count
6
Evaluate dependency on package factoextra
Updated
3 years ago
Handling of missing values in PCA plots
Updated
3 years ago
Comments count
3
Issue with results table: for pvalues that are NA, adj.pvalue is 0
Closed
3 years ago
Comments count
2
Error in dataProcess(raw = dmss, normalization = FALSE, fillIncompleteRows = TRUE
Closed
3 years ago
Comments count
5
artmsAnalysisQuantifications error
Closed
3 years ago
Comments count
5
question about User defined PTM
Closed
3 years ago
Comments count
4
Support normalization using multiple reference proteins
Closed
3 years ago
Comments count
4
artmsEvidenceToSaintExpress: MISSING LENGTHS WITH THE MEDIAN LENGTH FROM THE DATASET
Updated
3 years ago
Comments count
1
Add warning text for PCA plot
Updated
3 years ago
Add plot of distribution of Intensities (pre and post normalization)
Updated
3 years ago
Plots: print gene name when available instead of protein code
Updated
3 years ago
Implement acetylation analysis
Closed
4 years ago
QCbasic: Improve correlation matrix plots
Closed
4 years ago
Fix warning: No summary function supplied, defaulting to `mean_se()`
Closed
4 years ago
Fix warning 8: Removed X rows containing missing values (geom_bar).
Closed
4 years ago
Replace data.table dcast and melt by tidyverse pivot_wider and pivot_long
Closed
4 years ago
Add contrast, results, and config RData objects for testing
Closed
4 years ago
Make the output name for QC plots consistent
Closed
4 years ago
Add symposium slides to vignette
Closed
4 years ago
Fix problems with SILAC data
Closed
4 years ago
Plots: Improve all plots printed labels when running too small or large datasets
Closed
4 years ago
Add printPDF option to all functions
Closed
4 years ago
Fix reproducibility plots from analysis of quantifications
Closed
4 years ago
read.table error on evidence.txt file
Closed
4 years ago
Comments count
3
Add 2d-density mz/rt map to QualityControlBasic
Updated
4 years ago
Upgrade gprofiler to gprofiler2
Updated
4 years ago
artmsQualityControlSummaryExtended() does not handle properly technical replicates
Updated
4 years ago
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