https://github.com/dmnfarrell/smallrnaseq
small rna-seq analysis package
https://github.com/dmnfarrell/smallrnaseq
bioinformatics genomics mirna python rna-seq sequencing smallrna
Last synced: about 2 months ago
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small rna-seq analysis package
- Host: GitHub
- URL: https://github.com/dmnfarrell/smallrnaseq
- Owner: dmnfarrell
- License: gpl-3.0
- Created: 2014-12-15T22:58:05.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2022-11-07T23:57:24.000Z (over 2 years ago)
- Last Synced: 2025-04-13T09:54:59.255Z (about 2 months ago)
- Topics: bioinformatics, genomics, mirna, python, rna-seq, sequencing, smallrna
- Language: Python
- Homepage:
- Size: 8.32 MB
- Stars: 30
- Watchers: 4
- Forks: 19
- Open Issues: 6
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Metadata Files:
- Readme: README.md
- Changelog: CHANGES
- License: LICENSE
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README
# smallrnaseq - tool for analysis of small RNA sequencing data
smallrnaseq is a Python package that integrates some of the standard approaches for convenient pre-processing, quantification and analysis of small RNAs. It includes a [command line interface](https://github.com/dmnfarrell/smallrnaseq/wiki/Command-line-interface) used in conjunction with a configuration file. Hence knowledge of Python is not a necessity for using this software. The aim is to provide convenience but with enough configuration to allow some flexibility. Supported on linux and OSX.
Functionality includes:
* command line interface
* ability to use several different short read aligners, (currently bowtie or subread)
* counting of mapped reads to annotated sequences or genomic features
* counting of miRNAs and isomiRs
* novel miRNA prediction
* running multiple files in a batch
* use of several normalization methods
### Usage
Up to date documentation is at http://smallrnaseq.readthedocs.io
There is a video tutorial at https://youtu.be/m24cuLyTqg0
### Installation
```pip install smallrnaseq```
or
```pip install -e git+https://github.com/dmnfarrell/smallrnaseq.git#egg=smallrnaseq```
See the [installation page](http://smallrnaseq.readthedocs.io/en/latest/description.html#installation) for more details
### Python Dependencies
* Numpy
* Pandas
* Matplotlib
* HTSeq
* Seaborn
* bx-python
* scikit-learn