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simdms

Deep mutational scanning dataset simulator.

https://github.com/fowlerlab/simdms

Science Score: 62.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: biorxiv.org, zenodo.org
  • ○
    Academic email domains
  • ✓
    Institutional organization owner
    Organization fowlerlab has institutional domain (faculty.washington.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.3%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Deep mutational scanning dataset simulator.

Basic Info
  • Host: GitHub
  • Owner: FowlerLab
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 20.5 KB
Statistics
  • Stars: 4
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Created almost 9 years ago · Last pushed over 4 years ago
Metadata Files
Readme License Citation

README.md

DOI

simdms

simdms is a script for simulating deep mutational scanning data. These datasets are intended to be analyzed using Enrich2. For more information or to cite simdms, please refer to Enrich2: a statistical framework for analyzing deep mutational scanning data.

Dependencies

simdms runs on Python 2.7 and requires the following packages:

  • NumPy version 1.10.4 or higher
  • SciPy version 0.16.0 or higher
  • pandas version 0.18.0 or higher
  • PyTables version 3.2.0 or higher

We recommend using a scientific Python distribution such as Anaconda or Enthought Canopy to install and manage dependencies. PyTables may not be installed when using the default settings for your distribution. If you encounter errors, check that the tables module is present.

To use simdms, git clone or download the repository and run python simdms.py config.json from its root directory. simdms takes a json-formatted configuration file as the command line argument.

Questions?

Please use the GitHub Issue Tracker to file bug reports or request features.

simdms was written by Alan F Rubin and Hannah Gelman.

Owner

  • Name: Fowler Lab
  • Login: FowlerLab
  • Kind: organization
  • Email: dfowler@uw.edu
  • Location: Seattle, Washington, USA

Laboratory of Douglas M. Fowler in the Department of Genome Sciences at the University of Washington.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Rubin"
  given-names: "Alan F"
  orcid: "https://orcid.org/0000-0003-1474-605X"
- family-names: "Gelman"
  given-names: "Hannah"
title: "simdms"
version: 0.1
doi: 10.5281/zenodo.546311
date-released: 2017-04-15
url: "https://github.com/FowlerLab/simdms"
preferred-citation:
  type: article
  authors:
  - family-names: "Rubin"
    given-names: "Alan F"
    orcid: "https://orcid.org/0000-0003-1474-605X"
  - family-names: "Gelman"
    given-names: "Hannah"
  - family-names: "Lucas"
    given-names: "Nathan"
  - family-names: "Bajjalieh"
    given-names: "Sandra M"
  - family-names: "Papenfuss"
    given-names: "Anthony T"
    orcid: "https://orcid.org/0000-0002-1102-8506"
  - family-names: "Speed"
    given-names: "Terence P"
    orcid: "https://orcid.org/0000-0002-5403-7998"
  - family-names: "Fowler"
    given-names: "Douglas M"
    orcid: "https://orcid.org/0000-0001-7614-1713"
  doi: "10.1186/s13059-017-1272-5"
  journal: "Genome Biology"
  month: 8
  start: 150
  title: "A statistical framework for analyzing deep mutational scanning data"
  issue: 1
  volume: 18
  year: 2017

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