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PSLDoc2

PSLDoc2 is the extended version of PSLDoc and it is implemented based on the nextflow framework.
https://github.com/paoloditommaso/nextflow

web site:
http://tcoffee.crg.cat/psldoc2

Dependencies

Configuration

Extra R libraries can be specified using the R_LIBS environment variables. Add this variable
to the nextflow.config file in the project root folder, as shown in the following example:

env {
  R_LIBS = "$PWD/r_libs/"
}

Stand alone version

Prediction

  1. localizaiton
  2. nuclear
    • uclear裡的子胞器(sub-localization)是針對細胞核這位置再繼續細分下去,也有sub-mitochondrian等子胞器的分類
  3. protein function
    • Kinase

Build your own model

  1. training phase

    • psldoc2-train.nf -> CA_train+nFoldValidation.R
    • input: model.fasta
    • output: model.tfpssm, plot_model.json, accuracy-nfold.csv, predict.csv (CA dims)

       $ nextflow psldoc2_train.nf --model=../../../data/PSL/PSORTb3.0/Archaeal.fasta --fold_num=5
      
  2. predicting phase

    • psldoc2-pred.nf -> CA_pred.R (query.fasta, model.tfpssm, CA dims)
    • input: query.fasta, model.tfpssm
    • output: plot_query.json, query.pred

       $ nextflow psldoc2_pred.nf --query small.fa --model data/prokaryotic/Archaeal.tfpssm --CA_dim 36
      
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cbcrg
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