Statistical analysis of RNA-Seq, PAT-Seq, microarray data using linear models.
Python R Shell
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
backyard
doc
fitnoise
.gitignore
CHANGES
LICENSE
README.md
TODO
freshen.sh
make_virtualenv.sh
requirements.txt
setup.py

README.md

Fitnoise

Fitnoise is a Python 2 library for statistical analysis of RNA-Seq, PAT-Seq, and microarray data using linear models.

An R wrapper is provided to allow access from R.

Fitnoise uses the Theano deep-learning library for speed.

Fitnoise is developed by Dr. Paul Harrison for the RNA Systems Biology Laboratory, Monash University.

Overview:

Documentation:

Download:

Links:

Installing into a virtualenv from source

This is the easiest way to try out Fitnoise.

The following creates a virtualenv in directory venv for both Python and R:

./make_virtualenv.sh venv

To freshen the virtualenv after pulling a new version of Fitnoise from github or hacking on the code:

./freshen.sh venv

Installing globally

On the python side, Fitnoise requires Theano. On the R side, Fitnoise requires rPython, and jsonlite, and limma.

Installing dependencies:

apt-get install python-pip python-numpy python-scipy r-base
# (or whichever package manager is appropriate to your Linux distribution)
# (MacOS users can use brew and Anaconda Python)

pip install --upgrade git+git://github.com/Theano/Theano.git

R
  install.packages(c("rPython", "jsonlite"))
  source("http://bioconductor.org/biocLite.R")
  biocLite("limma")

To install Fitnoise with pip:

pip install --upgrade fitnoise

python -m fitnoise
# This prints out instructions to install the R component

Alternatively, to install Fitnoise from source:

python setup.py install
R CMD INSTALL fitnoise

Alternatively, to install the development version of Fitnoise directly from github:

pip install --upgrade 'git+https://github.com/pfh/fitnoise.git#egg=fitnoise'

R
  install.packages("devtools")
  devtools::install_github("pfh/fitnoise", subdir="fitnoise")

References

Fitnoise re-implements various features of the limma Bioconductor package:

http://bioinf.wehi.edu.au/limma/