riboraptor : a pipeline for analysing ribosome profiling data

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Python package to analyse ribosome profiling data

Free software: BSD license
Documentation: http://saketkc.github.io/riboraptor/

Installation

Setting up conda

Install conda, the best way to install it is with the Miniconda package.The Python 3 version is recommended.
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

Install aspera connect
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(".")

Features

See: http://saketkc.github.io/riboraptor/cmd-manual.html

History

0.2.0 (04-23-2018)

First release on PyPI.

Metadata

Release files for riboraptor 0.2.2

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Source distribution (sdist)

Source distribution for riboraptor 0.2.2
File	Size	Uploaded	Provenance
riboraptor-0.2.2.tar.gz	23.2 MB	Apr 27, 2018	Without provenance	Details

Built distribution (wheel)

Table of built distributions (wheels) for riboraptor 0.2.2
File	Interpreter	ABI	Platform	Reset
riboraptor-0.2.2-py2.py3-none-any.whl 7.7 MB Apr 27, 2018 Without provenance	Python 2, Python 3	none	any	Details

Total release size: 30.9 MB

Release files / riboraptor-0.2.2.tar.gz

Download URL	riboraptor-0.2.2.tar.gz
Size	23.2 MB
Tags	Source
SHA-256 checksum How to use checksums	`ae7a83ebe2670ad7efc4164ac27a416913b0e45eea07b3edf41fb8b6343e062e`
BLAKE2b-256 checksum How to use checksums	`bc19eb66cc4a633bf9febb94a22297bebc654fe2805f837aed2e355bee160848`
Upload date	Apr 27, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No

Release files / riboraptor-0.2.2-py2.py3-none-any.whl

Download URL	riboraptor-0.2.2-py2.py3-none-any.whl
Size	7.7 MB
Tags	Python 2 Python 3
SHA-256 checksum How to use checksums	`e076ac9d094a2f7649b6e8fb51f709a334cb2abeda0c41d4fe75c8591a8bacc5`
BLAKE2b-256 checksum How to use checksums	`04ca14fd27cf78a6b0887766d8e076bf78085b610eac3788ffd409bee93d1809`
Upload date	Apr 27, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No

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This release

0.2.2 This release

Apr 27, 2018 2 release files No provenance

0.2.1

Apr 23, 2018 3 release files No provenance

riboraptor 0.2.2