Skip to main content

Python package to analyse ribosome profiling data

Project description

riboraptor : a pipeline for analysing ribosome profiling data

https://img.shields.io/pypi/v/riboraptor.svg https://travis-ci.org/saketkc/riboraptor.svg?branch=master

Python package to analyse ribosome profiling data

Installation

Setting up conda

  1. Install conda, the best way to install it is with the Miniconda package.The Python 3 version is recommended.
  2. Set up channels, It is important to add them in this order.
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Installing dependencies

conda create --name riboraptor python=3.6 matplotlib numpy pandas pybedtools \
pyBigWig pyfaidx pysam scipy seaborn statsmodels six click click-help-colors htseq biopython \
snakemake sra-tools star fastqc trim-galore ucsc-bedgraphtobigwig ucsc-bedsort

Installing riboraptor

source activate riboraptor
git clone git@github.com:saketkc/riboraptor.git
cd riboraptor
python setup.py install --single-version-externally-managed --record=/tmp/record.txt

Downloading datasets from SRA

  1. Install aspera connect
  2. Install additional dependencies
source activate riboraptor
conda install gcc
conda install -c r r=3.4.1
conda install -c bioconda bioconductor-annotationdbi bioconductor-geometadb
conda install -c r r-devtools

Since there is currently bug with bioconductor-sradb, we will install it from github

git clone https://github.com/seandavi/SRAdb
cd SRAdb

Run R, and install SRAdb within R use devtools

library(devtools)
devtools::install(".")

History

0.2.0 (04-23-2018)

  • First release on PyPI.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for riboraptor, version 0.2.2
Filename, size File type Python version Upload date Hashes
Filename, size riboraptor-0.2.2-py2.py3-none-any.whl (7.7 MB) File type Wheel Python version py2.py3 Upload date Hashes View
Filename, size riboraptor-0.2.2.tar.gz (23.2 MB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page