Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.1%) to scientific vocabulary
Keywords
Repository
Application for semi-automated genomic annotation.
Basic Info
- Host: GitHub
- Owner: hoffmangroup
- License: gpl-2.0
- Language: Shell
- Default Branch: master
- Homepage: http://segway.hoffmanlab.org/
- Size: 31.1 MB
Statistics
- Stars: 16
- Watchers: 3
- Forks: 7
- Open Issues: 99
- Releases: 4
Topics
Metadata Files
README.md
Segway
by Michael Hoffman michael.hoffman at utoronto dot ca
Description
The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Our software has extensive documentation and was designed from the outset with external users in mind. Researchers at other universities and institutes have already installed and used Segway for their own projects.
Please see the following URL for information, installation, and support: http://segway.hoffmanlab.org/
Documentation
Live documentation based on this repository can be found on Read the Docs.
Contributing
Contributions to Segway are always welcome and encouraged. See CONTRIBUTING for more information on how to get started.
License
Segway is free software: you can redistribute it and/or modify it under the terms of version 2 of the GNU General Public License as published by the Free Software Foundation.
Segway is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Contact
Please let us segway-l at listserv dot utoronto dot ca know if you have any comments on the installation or use of Segway, or file an issue on Github.
Owner
- Name: hoffmangroup
- Login: hoffmangroup
- Kind: organization
- Repositories: 15
- Profile: https://github.com/hoffmangroup
Citation (CITATION.cff)
cff-version: 1.2.0
title: Segway
version: 3.0.3
date-released: "2020-01-22"
message: If you use this software, please cite both the article from preferred-citation and the software itself.
abstract: This software implements a method of segmentation and genome annotation
authors:
- family-names: Hoffman
given-names: Michael M.
affiliation: "University Health Network"
orcid: "https://orcid.org/0000-0002-4517-1562"
license: GPL-2.0-only
repository-code: "https://github.com/hoffmangroup/segway"
url: "https://segway.hoffmanlab.org"
preferred-citation:
type: edited-work
title: Unsupervised pattern discovery in human chromatin structure through genomic segmentation
year: 2012
authors:
- family-names: Hoffman
given-names: Michael M.
affiliation: "University of Washington"
orcid: "https://orcid.org/0000-0002-4517-1562"
- family-names: Buske
given-names: Orion J.
affiliation: "University of Washington"
orcid: "https://orcid.org/0000-0002-9064-092X"
- family-names: Wang
given-names: Jie
affiliation: "University of Massachusetts Medical School"
- family-names: Weng
given-names: Zhiping
affiliation: "University of Massachusetts Medical School"
- family-names: Bilmes
given-names: Jeff A.
affiliation: "University of Washington"
orcid: "https://orcid.org/0000-0002-7372-8778"
- family-names: Noble
affiliation: "University of Washington"
orcid: "https://orcid.org/0000-0001-7283-4715"
given-names: William Stafford
doi: 10.1038/nmeth.1937
journal: "Nature Methods"
publisher:
name: "Nature Portfolio"
GitHub Events
Total
- Watch event: 3
- Issue comment event: 2
- Push event: 3
- Pull request event: 1
Last Year
- Watch event: 3
- Issue comment event: 2
- Push event: 3
- Pull request event: 1
Dependencies
- autolog
- colorbrewer
- drmaa >=0.4a3
- genomedata
- gmtk
- optbuild
- optplus
- path.py
- python 3.*
- segway
- six
- textinput
- ucsc-bedtobigbed
- colorbrewer >=0.2.0
- genomedata >=1.4.2
- optplus >=0.2.0
- textinput >=0.2.0
- actions/checkout v2 composite
- actions/upload-artifact v2 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- ubuntu latest build