bartongroup/Proteus

Issues

• Differences in proteusData when using readProteinGroups with different conditions

  #49 opened a year ago by WackerO
  0

• fetchFromUniProt error

  #48 opened a year ago by tfccheng
  1

• Not compatible with R version

  #47 opened a year ago by cstgermain4
  1

• Add proteus to bioconda

  #46 opened 2 years ago by WackerO
  3

• Error in limmaRatioDE function

  #45 opened 3 years ago by TaraBartolec
  1

• extract peptide/protein count

  #44 opened 4 years ago by francescocay
  1

• How to make protein table?

  #43 opened 4 years ago by yueli8
  0

• Error in normalizeData(LH) : Input data must be of class proteusData.

  #42 opened 4 years ago by yueli8
  0

• Normalize the data of SILAC

  #41 opened 4 years ago by yueli8
  2

• How to integrate Phospho (STY)Sites.txt into Proteus analysis?

  #40 opened 4 years ago by subwaystation
  0

• Saving plotFID_live and plotVolcano_live

  #39 opened 4 years ago by zillurbmb51
  2

• Gene names needed

  #17 opened 4 years ago by MarekGierlinski
  0

• Function readEvidenceFile doesn't work

  #35 opened 4 years ago by sago91
  2

• Replicates in the same mix?

  #29 opened 4 years ago by evertonjlima
  1

• About library

  #38 opened 4 years ago by ypriverol
  1

• Normalization with different number of samples in experiments

  #37 opened 5 years ago by PolinaLip
  0

• PCA function missing

  #33 opened 5 years ago by gurpreet-bioinfo
  3

• Setting different measure.cols for readProteinGroups

  #34 opened 5 years ago by cmysrobinso
  2

• Error in the extraction commands while retrieving ids

  #32 opened 5 years ago by gurpreet-bioinfo
  3

• Reduced number of entries from readProteinsGroups

  #31 opened 5 years ago by gurpreet-bioinfo
  2

• Vignettes do not install

  #30 opened 6 years ago by MarekGierlinski
  1

• Spike-in SILAC?

  #26 opened 6 years ago by vidaletal
  1

• Problem with parallel::mclapply on Windows

  #27 opened 6 years ago by Pam65
  3

• Error with makePeptideTable(evi, meta), Intensity not found

  #28 opened 6 years ago by Sabbalonn
  1

• Vignettes not installing?

  #25 opened 6 years ago by ar3781
  1

• Issues with phantom condition levels

  #24 opened 6 years ago by MarekGierlinski
  1

• PlotVolcano live condition (x-axis) label text

  #23 opened 6 years ago by ygyue
  3

• Reference and PRIDE dataset in TMT vignette are incorrect

  #22 opened 6 years ago by pwilmart
  2

• allowedUniprotColumns not exported

  #21 opened 6 years ago by MarekGierlinski
  1

• Choosing p-value column for volcano plot...

  #4 opened 6 years ago by nickschurch
  1

• Ngood in limmaDE should only contain two conditions

  #19 opened 6 years ago by MarekGierlinski
  1

• min.peptides should be 2 by default

  #18 opened 6 years ago by MarekGierlinski
  1

• makeProteinTable crashes with one condition

  #20 opened 6 years ago by MarekGierlinski
  1

• Libraries required

  #16 opened 7 years ago by MarekGierlinski
  1

• Crash when evidence without "Experiment" column provided

  #15 opened 7 years ago by MarekGierlinski
  1

• plotVolcano_life produces error message with peptide data

  #14 opened 7 years ago by MarekGierlinski
  1

• Make log transform for limmaDE a parameter and set default to log2

  #3 opened 7 years ago by nickschurch
  3

• no heatmaps in live.R functions

  #13 opened 7 years ago by Gasta88
  1

• Non-unique annotations

  #12 opened 7 years ago by MarekGierlinski
  1

• Dealing with peptides/proteins that aren't detected in all conditions...

  #6 opened 7 years ago by nickschurch
  2

• pep2prot table in peptides contains NAs

  #7 opened 7 years ago by MarekGierlinski
  1

• limma result: first column is always "protein"

  #8 opened 7 years ago by MarekGierlinski
  1

• significance threshold set in limmaDE

  #5 opened 7 years ago by nickschurch
  2

• plotPeptideCount labels y-axis as 'peptide' even with protein table

  #2 opened 7 years ago by nickschurch
  1

• Vignette doesn't import 'parallel'

  #1 opened 7 years ago by nickschurch
  1