biodavidjm/artMS

Issues

• Question about filtering conditions with MSstats quantification

  #197 opened a year ago by mstaniak
  2

• Could you please add MSStats removeFewMeasurements argument in the config.yaml?

  #196 opened 2 years ago by weixiandeng
  0

• Feature request: allow duplications for artmsMapUniprot2Entrez

  #195 opened 2 years ago by vivaciousvijaya
  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 opened 2 years ago by vivaciousvijaya
  0

• Error: "supply both 'x' and 'y' or a matrix-like 'x'"

  #193 opened 2 years ago by tsveth
  3

• Question about SILAC data analysis

  #192 opened 3 years ago by giuliof95
  0

• Error: Assigned data `dfdc.final[[x]] - dfdc.final[[y]]` must be compatible with existing data

  #190 opened 3 years ago by jfertaj
  11

• Problem about user-defined modification type

  #191 opened 3 years ago by Wang-Xuejun
  8

• Error in vecseq(f__, len__, if (allow.cartesian || notjoin || !anyDuplicated

  #184 opened 3 years ago by jfertaj
  15

• question about user modification

  #189 opened 3 years ago by hemingwang
  14

• Would be great to support additional PTMs in a way that doesn't require recoding artMS for each new PTM

  #168 opened 3 years ago by bpolacco
  0

• Add checkpoint to validate naming rules of the keys file

  #163 opened 4 years ago by biodavidjm
  0

• org.*.eg.db packages other than mouse/human are not in namespace

  #149 opened 5 years ago by bpolacco
  1

• Deprecate protein complex enrichment analysis

  #188 opened 3 years ago by biodavidjm
  0

• Replace gProfileR by gprofiler2

  #187 opened 3 years ago by biodavidjm
  0

• Remove negative values from ModelQC

  #186 opened 3 years ago by biodavidjm
  0

• New format of modifications from MaxQuant cause artmsProtein2SiteConversion to fail

  #166 opened 4 years ago by bpolacco
  4

• Fix: message of number of Intensity values = 0

  #185 opened 3 years ago by biodavidjm
  0

• Minor issue in artms_getMSstatsFormat default parameters, future bug maybe

  #167 opened 3 years ago by bpolacco
  1

• Add printPDF to analysis of Quantifications

  #165 opened 3 years ago by biodavidjm
  0

• Create folders

  #172 opened 3 years ago by biodavidjm
  0

• Issue with results-summary.xlsx (in "wide" tables, missing results get iLog2FC and iPvalue = 0)

  #175 opened 3 years ago by OlgaTSchubert
  2

• MSstats changes

  #181 opened 3 years ago by mstaniak
  6

• Evaluate dependency on package factoextra

  #183 opened 3 years ago by biodavidjm
  0

• Handling of missing values in PCA plots

  #171 opened 4 years ago by bpolacco
  3

• Issue with results table: for pvalues that are NA, adj.pvalue is 0

  #177 opened 3 years ago by OlgaTSchubert
  2

• Error in dataProcess(raw = dmss, normalization = FALSE, fillIncompleteRows = TRUE

  #180 opened 3 years ago by jfertaj
  5

• artmsAnalysisQuantifications error

  #179 opened 4 years ago by Monod79
  5

• question about User defined PTM

  #178 opened 4 years ago by hemingwang
  4

• Support normalization using multiple reference proteins

  #174 opened 4 years ago by OlgaTSchubert
  4

• artmsEvidenceToSaintExpress: MISSING LENGTHS WITH THE MEDIAN LENGTH FROM THE DATASET

  #173 opened 4 years ago by Skourtis
  1

• Add warning text for PCA plot

  #170 opened 4 years ago by biodavidjm
  0

• Add plot of distribution of Intensities (pre and post normalization)

  #161 opened 4 years ago by biodavidjm
  0

• Plots: print gene name when available instead of protein code

  #148 opened 5 years ago by biodavidjm
  0

• Implement acetylation analysis

  #144 opened 4 years ago by biodavidjm
  0

• QCbasic: Improve correlation matrix plots

  #151 opened 4 years ago by biodavidjm
  0

• Fix warning: No summary function supplied, defaulting to `mean_se()`

  #155 opened 4 years ago by biodavidjm
  0

• Fix warning 8: Removed X rows containing missing values (geom_bar).

  #154 opened 4 years ago by biodavidjm
  0

• Replace data.table dcast and melt by tidyverse pivot_wider and pivot_long

  #153 opened 4 years ago by biodavidjm
  0

• Add contrast, results, and config RData objects for testing

  #156 opened 4 years ago by biodavidjm
  0

• Make the output name for QC plots consistent

  #146 opened 4 years ago by biodavidjm
  0

• Add symposium slides to vignette

  #145 opened 4 years ago by biodavidjm
  0

• Fix problems with SILAC data

  #159 opened 4 years ago by biodavidjm
  0

• Plots: Improve all plots printed labels when running too small or large datasets

  #147 opened 4 years ago by biodavidjm
  0

• Add printPDF option to all functions

  #157 opened 4 years ago by biodavidjm
  0

• Fix reproducibility plots from analysis of quantifications

  #160 opened 4 years ago by biodavidjm
  0

• read.table error on evidence.txt file

  #162 opened 4 years ago by Deanho
  3

• Add 2d-density mz/rt map to QualityControlBasic

  #150 opened 5 years ago by biodavidjm
  0

• Upgrade gprofiler to gprofiler2

  #158 opened 5 years ago by biodavidjm
  0

• artmsQualityControlSummaryExtended() does not handle properly technical replicates

  #143 opened 5 years ago by biodavidjm
  0