| nohup command &>/dev/null & |
This code is referenced in the pathway enrichment workflow step Visualize.
Use R/Bioconductor to generate an [expression dataset (.txt)](http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#TXT:_Text_file_format_for_expression_dataset_.28.2A.txt.29 and phenotype file (.cls) for Enrichment Map.
This code is referenced in the pathway enrichment workflow step Get Data.
Use the TCGAbiolinks R/Bioconductor package to query the Genomic Data Commons (GDC) data portal for The Cancer Genome Atlas (TCGA) high-grade serous ovarian cancer (HGS-OvCa) RNA sequencing count data.
This code is referenced in the pathway enrichment workflow step Process Data.
Use the edgeR R/Bioconductor package to analyze RNA sequencing data for high-grade serous ovarian cancer (HGS-OvCa) from The Cancer Genome Atlas (TCGA) for differentially expressed genes.
| import os | |
| import fnmatch | |
| import json | |
| import pandas as pd | |
| def writeout(output_path, df): | |
| """ | |
| Write dataframe (df) to output path (output_path) | |
| """ | |
| directory = os.path.dirname(output_path) |
| import os | |
| import fnmatch | |
| import json | |
| import pandas as pd | |
| def writeout(output_path, df): | |
| """ | |
| Write dataframe (df) to output path (output_path) | |
| """ | |
| directory = os.path.dirname(output_path) |
This is for use in the Pathway Commons Guide TCGA Ovarian Cancer data set description.
Install conda
Create a conda environment named tcgaov. You can use the supplied environments.yml to quickly get started.
This is a sample test suite for the Pathway Commons web service written in python.
Each example query on the web service description page is called programmatically and a sanity test is performed on each response. A .csv report summarizing these responses is dumped to the parent directory:
You can add the github repository as a remote to your checked out gist repository.
$ git clone git://gist.github.com/1234.git
$ git remote add github [email protected]:ChrisJamesC/myNewProject.git
Push it to initialize the git on github
$ git push -u github master
This will also change the upstream of the branch, so github will be default.