Aggregation analysis of low frequency variants in breast cancer

• Aggregation analysis of low frequency variants in breast cancer
  • Publication
  • Data
  • Software
    • modified MONSTER binaries
    • modified mummy executables
  • Repository Content
    • Code
    • Outputs
  • Note

Publication

tba

Data

samples of European and diverse ancestry collected by the Breast Cancer Association Consortium

Software

modified MONSTER binaries

• purpose: mixed model for robust rare variant SNPset association testing
• original publication DOI: 10.1002/gepi.21775
• original code: hosted at university of chicago
• original documentation: MONSTER_v1.3_doc.pdf
• github repository for adopted binaries: https://github.com/stef-mueller/MONSTER

modified mummy executables

• purpose: wrapper creating MONSTER input and extracting SNPset containing coding and associated regulatory region variants per gene
• original publication DOI: 10.1038/s41467-018-07070-8
• original code: https://github.com/hmgu-itg/burden_testing
• github repository for adopted pipeline: https://github.com/stef-mueller/mummy_for_genotypes

Repository Content

Code

analysis code used to create publication outputs can be found in folder code

Outputs

analysis outputs including figures and tables can be found in folder data/output

Note

due to data privacy some input files regarding sample phneotypes are not made available in this public github repository