Analysis service for storing analyzed and custom gene sets.

Stores analysis from https://github.com/ucscXena/XenaGoWidget

Generated here: https://github.com/ucscXena/XenaAnalysisService

Installation

 $ yarn install

Running the app

 # development
 $ yarn run start

 # watch mode
 $ yarn run start:dev

 # production mode
 $ yarn run start:prod

Test

 # unit tests
 $ yarn run test

 # e2e tests
 $ yarn run test:e2e

 # test coverage
 $ yarn run test:cov

Analysis Layer (R/Viper)

Setup

  install.packages("BiocManager")
  install.packages("plumber")
  install.packages("viper")
  install.packages("Rook")
  install.packages("jsonlite")
  install.packages("R.utils")
  install.packages("stringr")

Analysis

Rscript analysis-wrapper.R ./Xena_manual_pathways.gmt ./TCGA-CHOL_logtpm_forTesting.tsv ./test_outfile.tsv BPA

Rscript analysis-wrapper.R  ./test-data/Xena_manual_pathways.gmt ./test-data/TCGA-CHOL_logtpm_forTesting.tsv ./test-data/test_outfile.tsv 

Server

  Rscript analysis-server.R
  curl -v -F tpmdata=@test-data/TCGA-CHOL_logtpm_forTesting.tsv -F gmtdata=@test-data/Xena_manual_pathways.gmt http://localhost:8000/bpa_analysis

Web Server

Uses plumber: https://www.rplumber.io/

install.packages("plumber")

Run server:

Rscript server.R

Test:

curl "http://localhost:8000/echo
curl "http://localhost:8000/echo?msg=hello
curl --data "a=4&b=3" "http://localhost:8000/sum"
curl --data '{"a":4, "b":5}' http://localhost:8000/sum