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<img src="https://github.com/gtrichard/deepStats/blob/master/docs/images/deepStats_logo.png?raw=true" width="720px" class="center">

## 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. |

[dsCompareCurves]: https://github.com/gtrichard/deepStats/wiki/dsCompareCurves
[dsComputeBEDDensity]: https://github.com/gtrichard/deepStats/wiki/dsComputeBEDDensity
[dsComputeGCCoverage]: https://github.com/gtrichard/deepStats/wiki/dsComputeGCCoverage

## 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](https://toolshed.g2.bx.psu.edu/view/gtrichard/deepstats_dscomparecurves/)

	a/README.md		b/README.md
1	[![CircleCI](https://circleci.com/gh/gtrichard/deepStats/tree/master.svg?style=shield)](https://circleci.com/gh/gtrichard/deepStats/tree/circleci-project-setup) [![Conda version](https://img.shields.io/badge/bioconda-0.4-success.svg)](https://anaconda.org/bioconda/deepstats) [![Downloads](https://img.shields.io/conda/dn/bioconda/deepstats.svg?style=flat)](https://anaconda.org/bioconda/deepstats) ![](https://img.shields.io/badge/lifecycle-experimental-orange.svg) [![DOI](https://zenodo.org/badge/189997890.svg)](https://zenodo.org/badge/latestdoi/189997890) [![GPL](https://img.shields.io/github/license/gtrichard/deepStats?color=lightgrey)](https://github.com/gtrichard/deepStats/blob/circleci-project-setup/LICENSE.txt)	1	[![CircleCI](https://circleci.com/gh/gtrichard/deepStats/tree/master.svg?style=shield)](https://circleci.com/gh/gtrichard/deepStats/tree/circleci-project-setup) [![Conda version](https://img.shields.io/badge/bioconda-0.4-success.svg)](https://anaconda.org/bioconda/deepstats) [![Downloads](https://img.shields.io/conda/dn/bioconda/deepstats.svg?style=flat)](https://anaconda.org/bioconda/deepstats) ![](https://img.shields.io/badge/lifecycle-experimental-orange.svg) [![DOI](https://zenodo.org/badge/189997890.svg)](https://zenodo.org/badge/latestdoi/189997890) [![GPL](https://img.shields.io/github/license/gtrichard/deepStats?color=lightgrey)](https://github.com/gtrichard/deepStats/blob/circleci-project-setup/LICENSE.txt)
2		2
3		3
4		4
5	<img src="https://github.com/gtrichard/deepStats/blob/master/docs/images/deepStats_logo.png?raw=true" width="720px" class="center">	5	<img src="https://github.com/gtrichard/deepStats/blob/master/docs/images/deepStats_logo.png?raw=true" width="720px" class="center">
6		6
7	## Description	7	## Description
8		8
9	deepStats is a statistical and dataviz toolbox for deeptools, genomic signals, and more (GOterms, etc).	9	deepStats is a statistical and dataviz toolbox for deeptools, genomic signals, and more (GOterms, etc).
10		10
11	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.	11	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.
12		12
13	This is currently a Work In Progress	13	This is currently a Work In Progress
14		14
15	## Tools	15	## Tools
16		16
17	Below are quickly presented the available tools. Click on their name to access their respective documentation, or check the Wiki:	17	Below are quickly presented the available tools. Click on their name to access their respective documentation, or check the Wiki:
18	https://github.com/gtrichard/deepStats/wiki	18	https://github.com/gtrichard/deepStats/wiki
19		19
20	\| Tool name \| Description \|	20	\| Tool name \| Description \|
21	\| ----------------- \| ---------------------------------------------------- \|	21	\| ----------------- \| ---------------------------------------------------- \|
22	\| [dsCompareCurves] \| compares multiple genomic scores at multiple regions sets by bootstraps and per-bin distribution test. \|	22	\| [dsCompareCurves] \| compares multiple genomic scores at multiple regions sets by bootstraps and per-bin distribution test. \|
23	\| [dsComputeBEDDensity] \| computes BED files features density along the genome given a bin size, output as bedGraphs. \|	23	\| [dsComputeBEDDensity] \| computes BED files features density along the genome given a bin size, output as bedGraphs. \|
24	\| [dsComputeGCCoverage] \| calculates the GC% along the genome for bins of a given size in a memory efficient way. \|	24	\| [dsComputeGCCoverage] \| calculates the GC% along the genome for bins of a given size in a memory efficient way. \|
25		25
26	[dsCompareCurves]: https://github.com/gtrichard/deepStats/wiki/dsCompareCurves	26	[dsCompareCurves]: https://github.com/gtrichard/deepStats/wiki/dsCompareCurves
27	[dsComputeBEDDensity]: https://github.com/gtrichard/deepStats/wiki/dsComputeBEDDensity	27	[dsComputeBEDDensity]: https://github.com/gtrichard/deepStats/wiki/dsComputeBEDDensity
28	[dsComputeGCCoverage]: https://github.com/gtrichard/deepStats/wiki/dsComputeGCCoverage	28	[dsComputeGCCoverage]: https://github.com/gtrichard/deepStats/wiki/dsComputeGCCoverage
29		29
30	## Citation	30	## Citation
31		31
32	If you use deepStats in your work, please cite this repository using the following :	32	If you use deepStats in your work, please cite this repository using the following :
33		33
34	> Gautier RICHARD. (2019, August 6). gtrichard/deepStats: deepStats 0.3.1 (Version 0.3.1). Zenodo. https://doi.org/10.5281/zenodo.3336593	34	Gautier RICHARD. (2019, August 6). gtrichard/deepStats: deepStats 0.3.1 (Version 0.3.1). Zenodo. https://doi.org/10.5281/zenodo.3336593
35		35
36	## Installation	36	## Installation
37		37
38	- As a command-line tool through Conda	38	- As a command-line tool through Conda
39		39
40	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.	40	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.
41	```	41	```
42	conda create -n mamba -c conda-forge mamba	42	conda create -n mamba -c conda-forge mamba
43	conda activate mamba	43	conda activate mamba
44	mamba create -n deepStats -c bioconda -c conda-forge deepstats	44	mamba create -n deepStats -c bioconda -c conda-forge deepstats
45	conda activate deepStats	45	conda activate deepStats
46	```	46	```
47		47
48	- As R Notebooks	48	- As R Notebooks
49		49
50	Currently, R notebooks are not up-to-date.	50	Currently, R notebooks are not up-to-date.
51		51
52	Install the following packages in your R environment:	52	Install the following packages in your R environment:
53	```	53	```
54	install.packages('optparse',repos = "http://cran.us.r-project.org")	54	install.packages('optparse',repos = "http://cran.us.r-project.org")
55	install.packages('boot',repos = "http://cran.us.r-project.org")	55	install.packages('boot',repos = "http://cran.us.r-project.org")
56	install.packages('ggplot2',repos = "http://cran.us.r-project.org")	56	install.packages('ggplot2',repos = "http://cran.us.r-project.org")
57	install.packages('cowplot',repos = "http://cran.us.r-project.org")	57	install.packages('cowplot',repos = "http://cran.us.r-project.org")
58	install.packages('tidyverse',repos = "http://cran.us.r-project.org")	58	install.packages('tidyverse',repos = "http://cran.us.r-project.org")
59	install.packages('dichromat',repos = "http://cran.us.r-project.org")	59	install.packages('dichromat',repos = "http://cran.us.r-project.org")
60	install.packages('purrr',repos = "http://cran.us.r-project.org")	60	install.packages('purrr',repos = "http://cran.us.r-project.org")
61	```	61	```
62		62
63	Then, access the R Notebooks stored in `deepStats/notebooks/` by cloning this repository:	63	Then, access the R Notebooks stored in `deepStats/notebooks/` by cloning this repository:
64	```	64	```
65	git clone https://github.com/gtrichard/deepStats	65	git clone https://github.com/gtrichard/deepStats
66	```	66	```
67		67
68	- As Galaxy wrappers	68	- As Galaxy wrappers
69		69
70	You can install deepStats in a Galaxy instance through the [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/view/gtrichard/deepstats_dscomparecurves/)	70	You can install deepStats in a Galaxy instance through the [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/view/gtrichard/deepstats_dscomparecurves/)