| Name | qtl JSON |
| Version |
0.1.10
JSON |
| download |
| home_page | None |
| Summary | Utilities for analyzing and visualizing QTL data |
| upload_time | 2024-11-10 20:36:17 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | None |
| license | BSD 3-Clause License Copyright (c) 2019, The Broad Institute, Inc. and The General Hospital Corporation. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
quantitative
trait
loci
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
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| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
## pyQTL
pyQTL is a python module for analyzing and visualizing quantitative trait loci (QTL) data.
The following functionalities are provided:
* `qtl.annotation`: class for working with gene annotations; includes a [GTF](https://www.gencodegenes.org/pages/data_format.html) parser.
* `qtl.coloc`: Python implementation of core functions from the [R COLOC package](https://github.com/chr1swallace/coloc).
* `qtl.io`: functions for reading/writing BED and GCT files.
* `qtl.locusplot`: functions for generating LocusZoom-style regional association plots.
* `qtl.pileup`: functions for visualizing QTL effects in read pileups from, e.g., RNA-seq data.
* `qtl.plot`: plotting functions for QTLs.
### Install
You can install pyQTL using pip:
```
pip3 install qtl
```
or directly from this repository:
```
$ git clone git@github.com:broadinstitute/pyqtl.git
$ cd pyqtl
# set up virtual environment and install
$ virtualenv venv
$ source venv/bin/activate
(venv)$ pip install -e .
```
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"description": "## pyQTL\n\npyQTL is a python module for analyzing and visualizing quantitative trait loci (QTL) data.\n\nThe following functionalities are provided:\n* `qtl.annotation`: class for working with gene annotations; includes a [GTF](https://www.gencodegenes.org/pages/data_format.html) parser.\n* `qtl.coloc`: Python implementation of core functions from the [R COLOC package](https://github.com/chr1swallace/coloc).\n* `qtl.io`: functions for reading/writing BED and GCT files.\n* `qtl.locusplot`: functions for generating LocusZoom-style regional association plots.\n* `qtl.pileup`: functions for visualizing QTL effects in read pileups from, e.g., RNA-seq data.\n* `qtl.plot`: plotting functions for QTLs.\n\n### Install\nYou can install pyQTL using pip:\n```\npip3 install qtl\n```\nor directly from this repository:\n```\n$ git clone git@github.com:broadinstitute/pyqtl.git\n$ cd pyqtl\n# set up virtual environment and install\n$ virtualenv venv\n$ source venv/bin/activate\n(venv)$ pip install -e .\n```\n",
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