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
Up to date documentation is at http://smallrnaseq.readthedocs.io
There is a video tutorial at https://youtu.be/m24cuLyTqg0
pip install smallrnaseq
or
pip install -e git+https://github.com/dmnfarrell/smallrnaseq.git#egg=smallrnaseq
See the installation page for more details
- Numpy
- Pandas
- Matplotlib
- HTSeq
- Seaborn
- bx-python
- scikit-learn