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

snap install smallrnaseq

See the installation page for more details

Python Dependencies

Numpy
Pandas
Matplotlib
HTSeq
Seaborn
bx-python
scikit-learn