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 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 for more details

Python Dependencies

• Numpy
• Pandas
• Matplotlib
• HTSeq
• Seaborn
• bx-python
• scikit-learn