fgcz/prolfqua

Issues

• Statistical analysis in two conditions and 2 bioreplicates

  #91 opened 4 months ago by priyambial123
  0

• Lactylation modifications in MaxQuant

  #90 opened 4 months ago by hu-jie-max
  0

• prolfqua_MaxQuant output

  #89 opened 4 months ago by Heidelbergrabbit
  0

• build_model with continous fixed effect

  #88 opened 4 months ago by nomascus
  0

• Please provide an example how to create input data by hand

  #78 opened 6 months ago by chhh
  9

• how to enter a data table

  #79 opened 6 months ago by AryLech
  1

• Apply moderation to merged contrasts or to linear model only?

  #82 opened 5 months ago by Roman-Si
  1

• How can I re-arrange my samples in a plot in prolfqua

  #81 opened 5 months ago by jjGG
  1

• Track gap filling / imputed values

  #80 opened 6 months ago by wolski
  0

• tidyMQ_ProteinGroups fiunction is not working

  #77 opened 6 months ago by animesh
  3

• Contrast function mixes conditions in WaldTest output

  #71 opened 6 months ago by Roman-Si
  5

• simulate additional data

  #75 opened 7 months ago by wolski
  0

• remove dependencies from basic model and interaction model

  #74 opened 7 months ago by wolski
  0

• review ContrastsMissing get_contrasts

  #70 opened 7 months ago by wolski
  3

• remove dependecy on DT

  #72 opened 7 months ago by wolski
  0

• remove Contrasts$get_linfct() from Contrast Interface

  #32 opened 8 months ago by wolski
  1

• Reduce package size

  #58 opened 8 months ago by wolski
  2

• color densities using factor variable

  #63 opened a year ago by wolski
  0

• Issue with setup_analysis in comparing2groups vignette

  #68 opened 10 months ago by jrhougland
  11

• volcano plot with fixed ylim (scales) cannot be "freed up" with scales="free"

  #67 opened 10 months ago by jjGG
  5

• add in-silico talk

  #65 opened 10 months ago by cpanse
  1

• Glm support

  #64 opened a year ago by wolski
  1

• integrate proDA

  #25 opened 3 years ago by wolski
  2

• missing presence show using venn diagram

  #28 opened a year ago by wolski
  3

• add unit/class/function tests

  #35 opened a year ago by cpanse
  0

• Citation points to bioRxiv

  #61 opened a year ago by micwij
  1

• FragPipe v.19.1 combined_protein output not working with prolfqua::tidy_FragPipe_combined_protein

  #57 opened 2 years ago by mart5176
  1

• Sample Rscript to process fragpipe lfqMBR outputfile

  #56 opened 2 years ago by BenSamy2020
  1

• Unify naming conventions

  #36 opened 2 years ago by cpanse
  3

• Error with setup_analysis()

  #54 opened 2 years ago by amechakra
  4

• Error at normalisation step

  #55 opened 2 years ago by clawless-inoviv
  5

• DiaNN read report function

  #53 opened 2 years ago by clawless-inoviv
  3

• Remove plot_FDPvsTPR from Benchmark

  #52 opened 2 years ago by wolski
  0

• Add Precision Recall plot to Benchmark class

  #51 opened 2 years ago by wolski
  0

• Spellcheck text in vignettes

  #49 opened 2 years ago by wolski
  1

• Broken links to Article source files

  #48 opened 2 years ago by fabianegli
  1

• Rename ContrastsSimpleImpute to ContrastsMissing.

  #50 opened 2 years ago by wolski
  0

• Add unit test for Contrasts parser

  #44 opened 2 years ago by cpanse
  0

• covr - Test Coverage for prolfqua

  #34 opened 2 years ago by cpanse
  2

• LICENSE

  #20 opened 2 years ago by cpanse
  1

• Simple Impute - if mean below 10% - diff to be estimated at 0

  #29 opened 3 years ago by jjGG
  2

• Add function to summarize significant fold changes to ContrastPlotter

  #27 opened 3 years ago by wolski
  0

• add heatmap with only sample wise clustering

  #26 opened 3 years ago by wolski
  0

• Export analysis results to ExpressionSet and ExpressionSetViewer

  #22 opened 4 years ago by wolski
  0

• Error Handling: Contrast and model specification

  #24 opened 3 years ago by jjGG
  0

• manage bioc submission

  #21 opened 3 years ago by cpanse
  1

• More descriptive axis labels for the MA plot

  #23 opened 3 years ago by fabianegli
  4

• Ion Quant error: Index out of bounds for length 10001

  #17 opened 4 years ago by jjGG
  1

• Protein Boxplot/ supervised heatmap

  #16 opened 4 years ago by wolski
  0

• Example run scripts for MSFragger and MaxQuant.

  #15 opened 5 years ago by wolski
  1