knowengdev/gene_prioritization_pipeline repository overview

⁠KnowEnG's Gene Prioritization Pipeline

This is the Knowledge Engine for Genomics (KnowEnG), an NIH, BD2K Center of Excellence, Gene Prioritization Pipeline.

This pipeline ranks the rows of a given spreadsheet, where spreadsheet's rows correspond to gene-labels and columns correspond to sample-labels. The ranking is based on correlating gene expression data (network smoothed) against pheno-type data.

There are four prioritization methods that one can choose from:

Note: all of the correlation methods mentioned above use the Pearson or t-test correlation measure method.

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⁠How to run this pipeline's docker image with Our data

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1. Install Docker - follow the instructions in this link. ============

Install Docker Engine⁠

1. Get the current Docker Image. On the command line with internet connection: ============

docker pull knowengdev/gene_prioritization_pipeline: 11_15_2018

1. Create or change to a directory to hold the output data. ============

mkdir local_results and / or cd local_results

1. Start the docker image connected to the (local_results) directory. =========== docker run -v local_results:/home/test/run_dir -it knowengdev/gene_prioritization_pipeline: 11_15_2018

2. At the docker image command prompt change to the test directory. =========== .../home# cd test

3. Set up the environment. ============= .../home/test# make env_setup

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1. Use one of the following "make" commands to select and run a clustering option: ===========

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⁠How to run this pipeline with Your data.

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*** Perform steps 1-3 as described above and use the local_results directory ***

⁠Create a custom YAML file, move that and your spreadsheet to the local_results directory

*** see the git hub directions *** Gene Prioritization ReadMe on github⁠

*** make sure file named by YAML key "spreadsheet_name_full_path:" is in your local_results directory *** *** the path-names inside docker depend on the way you "mount" the run directory in step 4 *** *** therefore you may have to change the YAML path's to ../../ instead of ../ *** *** make sure your custom YAML file is in the local_results directory ***

1. Start docker with the container connected to your (local_results) directory. =========== docker run -v local_results:/home/test/run_dir -it knowengdev/gene_prioritization_pipeline: 11_15_2018

2. Change to the directory mounted in step 4. =========== .../home# cd ./test/run_dir .../home/test/run_dir# ls

*** the files in the local_results directory will be visible in this directory ***

1. Run Gene Prioritization with the options in your custom YAML file. ========= python3 ../../src/gene_prioritization.py -run_directory ./ -run_file zTEMPLATE_GP_BENCHMARKS.yml

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⁠Description of "run_parameters" file

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⁠Description of Output files saved in results directory

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• Any method saves separate files per phenotype with name

{phenotype}_{method}_{correlation_measure}_{timestamp}_viz.tsv

Genes are sorted in descending order based on visualization_score

• Any method saves sorted genes for each phenotype with name

ranked_genes_per_phenotype_{method}_{correlation_measure}_{timestamp}_download.tsv

• Any method saves spreadsheet with top ranked genes per phenotype with name

top_genes_per_phenotype_{method}_{correlation_measure}_{timestamp}_download.tsv