biodavidjm artMS issues

biodavidjm / artMS

Analytical R Tools for Mass Spectrometry

GNU General Public License v3.0

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issues

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Question about filtering conditions with MSstats quantification

#197 mstaniak opened 1 year ago
2
Could you please add MSStats removeFewMeasurements argument in the config.yaml?

#196 weixiandeng opened 1 year ago
0
Feature request: allow duplications for artmsMapUniprot2Entrez

#195 vivaciousvijaya opened 2 years ago
0
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

#194 vivaciousvijaya opened 2 years ago
0
Error: "supply both 'x' and 'y' or a matrix-like 'x'"

#193 tsveth closed 2 years ago
3
Question about SILAC data analysis

#192 giuliof95 opened 2 years ago
0
Problem about user-defined modification type

#191 Wang-Xuejun opened 2 years ago
8
Error: Assigned data `dfdc.final[[x]] - dfdc.final[[y]]` must be compatible with existing data

#190 jfertaj opened 3 years ago
11
question about user modification

#189 hemingwang opened 3 years ago
14
Deprecate protein complex enrichment analysis

#188 biodavidjm opened 3 years ago
0
Replace gProfileR by gprofiler2

#187 biodavidjm opened 3 years ago
0
Remove negative values from ModelQC

#186 biodavidjm opened 3 years ago
0
Fix: message of number of Intensity values = 0

#185 biodavidjm opened 3 years ago
0
Error in vecseq(f__, len__, if (allow.cartesian || notjoin || !anyDuplicated

#184 jfertaj closed 3 years ago
15
Evaluate dependency on package factoextra

#183 biodavidjm opened 3 years ago
0
Address recent MSstats changes

#182 biodavidjm closed 3 years ago
0
MSstats changes

#181 mstaniak closed 3 years ago
6
Error in dataProcess(raw = dmss, normalization = FALSE, fillIncompleteRows = TRUE

#180 jfertaj closed 3 years ago
5
artmsAnalysisQuantifications error

#179 Monod79 closed 3 years ago
5
question about User defined PTM

#178 hemingwang closed 3 years ago
4
Issue with results table: for pvalues that are NA, adj.pvalue is 0

#177 OlgaTSchubert closed 3 years ago
2
Added isoform functionality

#176 ekzp6 closed 3 years ago
1
Issue with results-summary.xlsx (in "wide" tables, missing results get iLog2FC and iPvalue = 0)

#175 OlgaTSchubert closed 3 years ago
2
Support normalization using multiple reference proteins

#174 OlgaTSchubert closed 3 years ago
4
artmsEvidenceToSaintExpress: MISSING LENGTHS WITH THE MEDIAN LENGTH FROM THE DATASET

#173 Skourtis opened 3 years ago
1
Create folders

#172 biodavidjm closed 3 years ago
0
Handling of missing values in PCA plots

#171 bpolacco opened 3 years ago
3
Add warning text for PCA plot

#170 biodavidjm opened 3 years ago
0
Feature/flexible ptm

#169 bpolacco closed 3 years ago
0
Would be great to support additional PTMs in a way that doesn't require recoding artMS for each new PTM

#168 bpolacco closed 3 years ago
0
Minor issue in artms_getMSstatsFormat default parameters, future bug maybe

#167 bpolacco closed 3 years ago
1
New format of modifications from MaxQuant cause artmsProtein2SiteConversion to fail

#166 bpolacco opened 4 years ago
4
Add printPDF to analysis of Quantifications

#165 biodavidjm closed 3 years ago
0
define mac.allsig etc. when enrich=FALSE

#164 bpolacco closed 4 years ago
0
Add checkpoint to validate naming rules of the keys file

#163 biodavidjm opened 4 years ago
0
read.table error on evidence.txt file

#162 Deanho closed 4 years ago
3
Add plot of distribution of Intensities (pre and post normalization)

#161 biodavidjm opened 4 years ago
0
Fix reproducibility plots from analysis of quantifications

#160 biodavidjm closed 4 years ago
0
Fix problems with SILAC data

#159 biodavidjm closed 4 years ago
0
Upgrade gprofiler to gprofiler2

#158 biodavidjm opened 4 years ago
0
Add printPDF option to all functions

#157 biodavidjm closed 4 years ago
0
Add contrast, results, and config RData objects for testing

#156 biodavidjm closed 4 years ago
0
Fix warning: No summary function supplied, defaulting to `mean_se()`

#155 biodavidjm closed 4 years ago
0
Fix warning 8: Removed X rows containing missing values (geom_bar).

#154 biodavidjm closed 4 years ago
0
Replace data.table dcast and melt by tidyverse pivot_wider and pivot_long

#153 biodavidjm closed 4 years ago
0
dont_check_names used for data.frame and data.table evidence_file

#152 bpolacco opened 4 years ago
2
QCbasic: Improve correlation matrix plots

#151 biodavidjm closed 4 years ago
0
Add 2d-density mz/rt map to QualityControlBasic

#150 biodavidjm opened 4 years ago
0
org.*.eg.db packages other than mouse/human are not in namespace

#149 bpolacco opened 4 years ago
1
Plots: print gene name when available instead of protein code

#148 biodavidjm opened 4 years ago
0