Small RNA-seq annotation
Project description
mirtop
---------
[![](https://travis-ci.org/miRTop/mirtop.svg?branch=master)](https://travis-ci.org/miRTop/mirtop#)
[![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
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/incubator/blob/master/format/definition.md
Chat
----
[Ask question, ideas](https://gitter.im/mirtop/Lobby#)
[Contributors to code](https://gitter.im/mirtop/devel)
Cite
---------
http://mirtop.github.io
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=$PATH:~/mirtop_env
conda install -c bioconda pysam pybedtools pandas biopython samtools
git clone http://github.com/miRTop/mirtop
cd mirtop
python setup.py develop
```
Quick start
-----------
Read complete commands at: https://mirtop.readthedocs.org
```
git clone mirtop
cd mirtop/data/example/annotate
mirtop gff --sps hsa --hairpin hairpin.fa --gtf hsa.gff3 -o test_out sim_isomir.bam
```
Output
------
The `mirtop gff` generates the GFF3 adapter format to capture miRNA variations. The output is explained [here](https://github.com/miRTop/incubator/blob/master/format/definition.md).
Contributors
------------
* [Lorena Pantano](https://github.com/lpantano) (Bioinformatic Core, Harvard Chan School, Boston, USA)
* [Shruthi Bhat Bandyadka](https://github.com/sbb25) (Partners Personalized Medicine, Cambridge MA, USA)
---------
[![](https://travis-ci.org/miRTop/mirtop.svg?branch=master)](https://travis-ci.org/miRTop/mirtop#)
[![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
Command line tool to annotate with a standard naming miRNAs e isomiRs.
This tool adapt the miRNA GFF3 format agreed on here: https://github.com/miRTop/incubator/blob/master/format/definition.md
Chat
----
[Ask question, ideas](https://gitter.im/mirtop/Lobby#)
[Contributors to code](https://gitter.im/mirtop/devel)
Cite
---------
http://mirtop.github.io
About
-----
Join the team: https://orgmanager.miguelpiedrafita.com/join/15463928
Read more: http://mirtop.github.io
Installation
------------
### Bioconda
`conda install mirtop -c bioconda`
### PIP
`pip install mirtop`
### develop version
Thes best solution is to install conda to get an independent enviroment.
```
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b -p ~/mirtop_env
export PATH=$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/example/annotate
mirtop gff --sps hsa --hairpin hairpin.fa --gtf hsa.gff3 -o test_out sim_isomir.bam
```
Output
------
The `mirtop gff` generates the GFF3 adapter format to capture miRNA variations. The output is explained [here](https://github.com/miRTop/incubator/blob/master/format/definition.md).
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)
Project details
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