computational-metabolomics/structToolbox

Issues

• Error occurs when plotting PLS feature importance

  #67 opened 10 months ago by Chuan-Jiang
  2

• [BUG] default predicted slot for tSNE is set to a slot that doesnt exist

  #66 opened a year ago by grlloyd
  0

• Possibilities to plot 3d PCA ?

  #65 opened 2 years ago by oolonek
  1

• pca_scores_plot: incorrect grey data ellipse when using two factors

  #16 opened 3 years ago by grlloyd
  0

• HSD parameter "unbalanced" never gets used

  #62 opened 3 years ago by grlloyd
  0

• add "mean" method for calculating fold change

  #57 opened 3 years ago by grlloyd
  1

• the threshold for fold change using "median" isnt applied correctly

  #56 opened 3 years ago by grlloyd
  1

• the alpha parameter for fold change isnt used

  #55 opened 3 years ago by grlloyd
  1

• provide documentation for struct object outputs

  #54 opened 3 years ago by grlloyd
  1

• report reasons for NA in ANOVA / ttest

  #51 opened 3 years ago by grlloyd
  0

• add option to use 'equal variance' in ttest

  #39 opened 3 years ago by grlloyd
  1

• add PLS scores plot for regression models

  #41 opened 4 years ago by grlloyd
  1

• RSD filter incorrectly states it removes feature below the threshold

  #36 opened 3 years ago by grlloyd
  1

• add details of pqn calculation to description

  #37 opened 3 years ago by grlloyd
  2

• report number of features used to compute the median for PQN

  #38 opened 3 years ago by grlloyd
  2

• pqn factor_name has no description

  #33 opened 4 years ago by grlloyd
  1

• filter_na_count documentation is confusing

  #14 opened 4 years ago by grlloyd
  1

• fold_change output params have no column names

  #34 opened 4 years ago by grlloyd
  0

• PLS model is reporting coefficients for the last component only

  #43 opened 4 years ago by grlloyd
  1

• ask user to install missing packages when object is created

  #42 opened 4 years ago by grlloyd
  0

• add selectivity ratio as an output for PLS objects

  #40 opened 4 years ago by grlloyd
  0

• mean of medians not working correctly

  #28 opened 4 years ago by grlloyd
  0

• filter_by_name doesn't work with model_train

  #23 opened 4 years ago by grlloyd
  0

• make d-statistic/hotelling T2 a model object so that it can be used for filtering

  #25 opened 4 years ago by grlloyd
  0

• allow fixed value for glog_transform

  #10 opened 4 years ago by grlloyd
  1

• HSD doesnt handle missing groups well

  #13 opened 4 years ago by grlloyd
  1

• corr_coef fails when using with only one factor

  #9 opened 4 years ago by grlloyd
  0

• t-test fails when the factor_name column is characters instead of a factor

  #17 opened 4 years ago by grlloyd
  1

• fold change uses control group in the numerator

  #18 opened 4 years ago by grlloyd
  2

• log transform always uses base 10

  #15 opened 4 years ago by grlloyd
  1

• HCA dendrogram plotting group colours in wrong positions

  #7 opened 4 years ago by grlloyd
  2

• model.apply fails for a model sequence when seq_in is not equal to 'data'

  #8 opened 4 years ago by grlloyd
  1