Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/broadinstitute/regional_missense_constraint

Code to calculate regional missense constraint

https://github.com/broadinstitute/regional_missense_constraint

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization broadinstitute has institutional domain (www.broadinstitute.org)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

Code to calculate regional missense constraint

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 2.4 MB
Statistics
  • Stars: 13
  • Watchers: 12
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Created almost 7 years ago · Last pushed 8 months ago
Metadata Files
Readme License

README.md

Regional missense constraint and MPC

WARNING: This repository is under active development!

  • Regional missense constraint (RMC): Regional variability in tolerance to missense variation within a gene
  • Missense badness: Score that predicts deleteriousness of specific amino acid subsitution
  • MPC (Missense badness, Polyphen-2, and Constraint): Score that predicts missense variant deleteriousness by incorporating information about the specific amino acid substitution and the region around the variant

This repository contains code to determine RMC regions in gnomAD (currently v2.1.1) and use these regions to calculate both missense badness and MPC. All methods in this repository are adapted from Samocha et al (2017).

Repository structure:

  • regionalmissenseconstraint/rmc/pipeline: Contains pipeline scripts that call utility functions to generate results.
  • regionalmissenseconstraint/rmc/pipeline/twobreaks: Folder that contains scripts to search for two simultaneous breaks; see `regionalmissenseconstraint/rmc/pipeline/twobreaks/README.md`.
  • regionalmissenseconstraint/rmc/utils: Contains utility functions that prepare input data or calculate results (RMC, missense badness, MPC).

Regional missense constraint

Flowchart

Inputs: * Hail Table with all possible missense variants in the human exome (called VEP context) * gnomAD v2.1.1 public sites Hail Table

Output: * Hail Table annotated with RMC regions and filtered to curated transcripts; removed any transcripts following this criteria

Scripts:

  • pipeline/regional_constraint.py: Pipeline code that prepares input Table, searches for first single/additional single breaks, and merges finalized results.
  • pipeline/twobreaks: See `regionalmissenseconstraint/rmc/pipeline/twobreaks/README.md` for explanation of scripts in this folder.
  • utils/generic.py: Utility functions that help prepare data for calculations.
  • utils/constraint.py: Utility functions that calculate RMC results.

Missense badness

Scripts

  • pipeline/calculatemissensebadness.py: Pipeline code that prepares input Table and calculates missense badness score.
  • utils/missense_badness.py: Utility functions that prepare data for calculations and calculates missense badness.

MPC

Scripts

  • pipeline/calculate_mpc.py: Pipeline code that prepares input Table, calculates MPC, and annotates given input Table with MPC score.
  • utils/mpc.py: Utility functions that prepare data for calculations, creates MPC model regressions, and calculates MPC.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Watch event: 1
  • Delete event: 1
  • Push event: 28
  • Pull request review event: 38
  • Pull request review comment event: 42
  • Pull request event: 5
  • Create event: 3
Last Year
  • Watch event: 1
  • Delete event: 1
  • Push event: 28
  • Pull request review event: 38
  • Pull request review comment event: 42
  • Pull request event: 5
  • Create event: 3

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 41
  • Total pull requests: 127
  • Average time to close issues: 7 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 2.83
  • Average comments per pull request: 0.11
  • Merged pull requests: 121
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ch-kr (17)
  • gtiao (5)
  • gmerolli00 (1)
  • ryshi06 (1)
Pull Request Authors
  • ch-kr (87)
  • illusional (3)
  • Ruchit10 (2)
Top Labels
Issue Labels
Epic (9)
Pull Request Labels

Dependencies

requirements-dev.txt pypi
  • black ==22.3.0 development
  • pre-commit ==2.10.1 development
  • pydocstyle ==6.0.0 development
  • pylint * development
  • pytest ==6.2.3 development
requirements.txt pypi
  • hail *
.github/workflows/ci.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
rmc/resources/docker/Dockerfile docker
  • 'google/cloud-sdk slim' build
pyproject.toml pypi
requirements-dev.in pypi
  • autopep8 ==2.0.2 development
  • black ==23.7.0 development
  • isort ==5.12.0 development
  • pre-commit * development
  • pydocstyle ==6.1.1 development
  • pylint * development
  • pytest ==7.4.0 development