smartgamer / deepstats

deepStats: a stastitical toolbox for deeptools and genomic signals

Description

deepStats is a statistical and dataviz toolbox for deeptools, genomic signals, and more (GOterms, etc).

It aims at providing statistical analyses and streamlining the production of high quality, color-blind friendly, and fully customisable plots (up to the fonts!) for your classic genomic datasets (.bed, .bigwig, gene lists). The goal of deepStats is thus to significantly decrease the amount of time spent in Inkscape/Illustrator to get publication ready plots, and decreasing the research time allotted to finding proper statistical analyses for your genomic signals and datasets. It also aims at giving tools to complement deepTools functions.

This is currently a Work In Progress

Tools

Below are quickly presented the available tools. Click on their name to access their respective documentation, or check the Wiki: https://github.com/gtrichard/deepStats/wiki

Tool name	Description
dsCompareCurves	compares multiple genomic scores at multiple regions sets by bootstraps and per-bin distribution test.
dsComputeBEDDensity	computes BED files features density along the genome given a bin size, output as bedGraphs.
dsComputeGCCoverage	calculates the GC% along the genome for bins of a given size in a memory efficient way.

Citation

If you use deepStats in your work, please cite this repository using the following :

Gautier RICHARD. (2019, August 6). gtrichard/deepStats: deepStats 0.3.1 (Version 0.3.1). Zenodo. https://doi.org/10.5281/zenodo.3336593

Installation

• As a command-line tool through Conda

deepStats is easily deployable as a command-line tool with conda. Use the following command to create a virtual env for deepStats. Don't install deepStats in your base env nor in an environment containing other tools. The installation can be quite long using the regular conda create command, this is thus recommended to use mamba create instead.

conda create -n mamba -c conda-forge mamba
conda activate mamba
mamba create -n deepStats -c bioconda -c conda-forge  deepstats
conda activate deepStats

• As R Notebooks

Currently, R notebooks are not up-to-date.

Install the following packages in your R environment:

install.packages('optparse',repos = "http://cran.us.r-project.org")
install.packages('boot',repos = "http://cran.us.r-project.org")
install.packages('ggplot2',repos = "http://cran.us.r-project.org")
install.packages('cowplot',repos = "http://cran.us.r-project.org")
install.packages('tidyverse',repos = "http://cran.us.r-project.org")
install.packages('dichromat',repos = "http://cran.us.r-project.org")
install.packages('purrr',repos = "http://cran.us.r-project.org")

Then, access the R Notebooks stored in deepStats/notebooks/ by cloning this repository:

git clone https://github.com/gtrichard/deepStats

• As Galaxy wrappers

You can install deepStats in a Galaxy instance through the Galaxy Tool Shed