No description, website, or topics provided.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
TCGA_PAN/SCRIPTS
LICENSE.txt
README.md
achilles.r
cnamap.r
compare.r
expression.r
methylationmap.r
plotting.r
preprocessTCGA.r
scoring.r
sommut.r
survival.r
tcga_synapse.r
uploadResultsSynapse.r
utils.r

README.md

OncoScape

OncoScape is a package for gene prioritization in the R statistical programming environment. The analysis is run in a contrast fashion, i.e. always two groups of samples are compared with each other. Examples include:

  • tumors vs. normals
  • cell lines vs. normals
  • treatment responders vs resistant
  • samples with mutations in gene X vs wild type

Currently, analyses of five data types are implemented in OncoScape:

  1. gene expression
  2. DNA copy number
  3. DNA methylation
  4. mutation
  5. shRNA knock-down data

Aberrations in each gene are called for each data type separately and scored as 0 (no aberration found) or 1 (aberration found). These scores are summed across data types to give the final score. OncoScape differentiates between activating (oncogene-like) and inactivating (tumor suppressor-like) aberrations and calculates independent scores for both directions. It is possible to run the analysis on any combination of these data types.

Analysis workflow

The analysis proceeds in four steps: 0. data import

  1. calculate statistics (using "do*Analysis" methods)
  2. filtering and scoring (using "summarize*" methods)
  3. plotting of results

Example scripts for putting everything together are:

  • TCGA_PAN/SCRIPTS/load_tcga_pancancer_data.r
  • TCGA_PAN/SCRIPTS/prioritize_tcga_step1.r
  • TCGA_PAN/SCRIPTS/prioritize_tcga_step2.r
  • TCGA_PAN/SCRIPTS/plot*

Source files

  • achilles.r: functions to analyze data from Project Achilles (http://www.broadinstitute.org/achilles)
  • cnamap.r: functions to analyze copy number data
  • compare.r: functions for comparing OncoMap results from two different runs
  • expression.r: functions to analyze gene expression data
  • methylationmap.r: functions to analyze DNA methylation data
  • plotting.r: functions for plotting results
  • preprocessTCGA.r: functions for preprocessing data from the TCGA pancancer project
  • scoring.r: functions for calculating final scores
  • sommut.r: functions to analyze somatic mutation data
  • survival.r: functions to analyze survival data (not used at the moment)
  • tcga_synapse.r: functions to download TCGA data from Sage Bionetwork's Synapse (www.synapse.org)
  • uploadResutlsSynapse.r: functions to upload result files to Synapse
  • utils.r: helper functions used by others in this project