# mirtop <img src="artwork/logo.png" width="80" height="80">
[](https://travis-ci.org/miRTop/mirtop#)
[](http://www.repostatus.org/#active)
[](https://www.biorxiv.org/content/10.1101/505222v1)
Command line tool to annotate with a standard naming miRNAs e isomiRs.
This tool adapt the miRNA GFF3 format agreed on here: https://github.com/miRTop/mirGFF3
Chat
----
[Ask question, ideas](https://gitter.im/mirtop/Lobby#)
[Contributors to code](https://gitter.im/mirtop/devel)
Cite
----
http://mirtop.github.io
Contributing
------------
Everybody is welcome to contribute, fork the `devel` branch and start working!
If you are interesting in miRNA or small RNA analysis, you can jump into the incubator issue pages to propose/ask or say hi:
https://github.com/miRTop/incubator/issues
About
-----
Join the team: https://orgmanager.miguelpiedrafita.com/join/15463928
Read more: http://mirtop.github.io
Installation
------------
### Bioconda
`conda install mirtop -c bioconda`
### PIP
`pip install mirtop`
### develop version
Thes best solution is to install conda to get an independent enviroment.
```
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env
export PATH=$PATH:~/mirtop_env
conda install -c bioconda pysam pybedtools pandas biopython samtools
git clone http://github.com/miRTop/mirtop
cd mirtop
python setup.py develop
```
Quick start
-----------
Read complete commands at: https://mirtop.readthedocs.org
```
git clone mirtop
cd mirtop/data
mirtop gff --sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out sim_isomir.bam
```
Output
------
The `mirtop gff` generates the GFF3 adapted format to capture miRNA variations. The output is explained [here](https://github.com/miRTop/mirGFF3).
Contributors
------------
* [Lorena Pantano](https://github.com/lpantano) (Bioinformatic Core, Harvard Chan School, Boston, USA)
* [Shruthi Bhat Bandyadka](https://github.com/sbb25) (Partners Personalized Medicine, Cambridge MA, USA)
* [Iñaki Martínez de Ilarduya](http://www.germanstrias.org/technology-services/high-performance-computing/contact/)(HPC core, IGTP, Badalona, Spain)
* Rafael Alis
* [Victor Barrera](https://github.com/vbarrera) (Bioinformatic Core, Harvard Chan School, Boston, USA)
* [Steffen Möller](https://github.com/smoe) (University of Rostock)
* [Kieran O'Neill](https://github.com/oneillkza)
* [Roderic Espin](Universitat Oberta de Barcelona)
Citizens
--------
Here we cite any person who has contribute somehow to the project different than through code development and/or
bioinformatic concepts.
Gianvito Urgese,
Jan Oppelt(CEITEC Masaryk University, Brno, Czech Republic),
Thomas Desvignes,
Bastian,
Kieran O'Neill (BC Cancer),
Charles Reid (University of California Davis),
Radhika Khetani (Harvard Chan School of Public Health),
Shannan Ho Sui (Harvard Chan School of Public Health),
Simonas Juzenas(CAU),
Rafael Alis (Catholic University of Valencia),
Aida Arcas (Instituto de Neurociencias (CSIC-UMH)),
Yufei Lin (Harvard University),
Victor Barrera(Harvard Chan School of Public Health),
Marc Halushka (Johns Hopkins University)
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"description": "# mirtop <img src=\"artwork/logo.png\" width=\"80\" height=\"80\">\n\n[](https://travis-ci.org/miRTop/mirtop#)\n[](http://www.repostatus.org/#active)\n[](https://www.biorxiv.org/content/10.1101/505222v1)\n\nCommand line tool to annotate with a standard naming miRNAs e isomiRs.\n\nThis tool adapt the miRNA GFF3 format agreed on here: https://github.com/miRTop/mirGFF3\n\nChat\n----\n\n[Ask question, ideas](https://gitter.im/mirtop/Lobby#)\n[Contributors to code](https://gitter.im/mirtop/devel)\n\nCite\n----\n\nhttp://mirtop.github.io\n\nContributing\n------------\n\nEverybody is welcome to contribute, fork the `devel` branch and start working!\n\nIf you are interesting in miRNA or small RNA analysis, you can jump into the incubator issue pages to propose/ask or say hi:\n\nhttps://github.com/miRTop/incubator/issues\n\nAbout\n-----\n\nJoin the team: https://orgmanager.miguelpiedrafita.com/join/15463928\n\nRead more: http://mirtop.github.io\n\nInstallation\n------------\n\n### Bioconda\n\n`conda install mirtop -c bioconda`\n\n### PIP\n\n`pip install mirtop`\n\n### develop version\n\nThes best solution is to install conda to get an independent enviroment.\n\n```\nwget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh\n\nbash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env\n\nexport PATH=$PATH:~/mirtop_env\n\nconda install -c bioconda pysam pybedtools pandas biopython samtools\n\ngit clone http://github.com/miRTop/mirtop\n\ncd mirtop\n\npython setup.py develop\n```\n\nQuick start\n-----------\n\nRead complete commands at: https://mirtop.readthedocs.org\n\n```\ngit clone mirtop\ncd mirtop/data\nmirtop gff --sps hsa --hairpin examples/annotate/hairpin.fa --gtf examples/annotate/hsa.gff3 -o test_out sim_isomir.bam\n```\n\nOutput\n------\n\nThe `mirtop gff` generates the GFF3 adapted format to capture miRNA variations. The output is explained [here](https://github.com/miRTop/mirGFF3).\n\nContributors\n------------\n\n* [Lorena Pantano](https://github.com/lpantano) (Bioinformatic Core, Harvard Chan School, Boston, USA)\n* [Shruthi Bhat Bandyadka](https://github.com/sbb25) (Partners Personalized Medicine, Cambridge MA, USA)\n* [I\u00f1aki Mart\u00ednez de Ilarduya](http://www.germanstrias.org/technology-services/high-performance-computing/contact/)(HPC core, IGTP, Badalona, Spain)\n* Rafael Alis\n* [Victor Barrera](https://github.com/vbarrera) (Bioinformatic Core, Harvard Chan School, Boston, USA)\n* [Steffen M\u00f6ller](https://github.com/smoe) (University of Rostock)\n* [Kieran O'Neill](https://github.com/oneillkza)\n* [Roderic Espin](Universitat Oberta de Barcelona)\n\nCitizens\n--------\n\nHere we cite any person who has contribute somehow to the project different than through code development and/or\nbioinformatic concepts.\n\nGianvito Urgese,\nJan Oppelt(CEITEC Masaryk University, Brno, Czech Republic),\nThomas Desvignes,\nBastian,\nKieran O'Neill (BC Cancer),\nCharles Reid (University of California Davis),\nRadhika Khetani (Harvard Chan School of Public Health),\nShannan Ho Sui (Harvard Chan School of Public Health),\nSimonas Juzenas(CAU),\nRafael Alis (Catholic University of Valencia),\nAida Arcas (Instituto de Neurociencias (CSIC-UMH)),\nYufei Lin (Harvard University),\nVictor Barrera(Harvard Chan School of Public Health),\nMarc Halushka (Johns Hopkins University)\n",
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