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Tools to process and analyze deep sequencing data.
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dpryan79 Release 3.3.1 (#872)
* copy changes from bgruening

* this file should not be here since years (#845)

* Develop (#827)

* Merged into the wrong branch without noticing :( (#814)

* use better conda link (#799)

* Estimated filtering fix (#813)

* oops

* fix testing and set a max number of filtered reads

* apparently a bunch of things were getting skipped

* fix wrappers

* update computeMatrix wrapper

* Decrease memory needs (#817)

* Use an iterator to not blow memory up

* Update a bit more

* The GC bias stuff is all deprecated, I'm not fixing that old code

* Cache resulting counts rather than just decreasing the bin size (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #816

* expose option

* Add a test using pseudocounts and skipZeroOverZero

* syntax

* Fix tests

* Make --skipZeroOverZero a galaxy macro and add to bigwigCompare

* [ci skip] a bit of formatting

* Fix #822 (#826)

* fixes linting issues (#837)

* this file should not be here since years

* Add Arabidopsis TAIR10 (A_thaliana_Jun_2009) (#853)

Using output from:
faCount A_thaliana_Jun_2009.fa 
#seq	len	A	C	G	T	N	cpg
Chr1	30427671	9709674	5435374	5421151	9697113	164359	697370
Chr2	19698289	6315641	3542973	3520766	6316348	2561	457572
Chr3	23459830	7484757	4258333	4262704	7448059	5977	559031
Chr4	18585056	5940546	3371349	3356091	5914038	3032	439585
Chr5	26975502	8621974	4832253	4858759	8652238	10278	630299
ChrC	154478	48546	28496	27570	49866	0	4639
ChrM	366924	102464	82661	81609	100190	0	13697
total	119667750	38223602	21551439	21528650	38177852	186207	2802193
hpc $ python
Python 2.7.11 (default, Jul 25 2019, 12:10:26) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-28)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 119667750-186207
119481543

* Fix python version in Azure tests  (#860)

* Develop (#827)

* Merged into the wrong branch without noticing :( (#814)

* use better conda link (#799)

* Estimated filtering fix (#813)

* oops

* fix testing and set a max number of filtered reads

* apparently a bunch of things were getting skipped

* fix wrappers

* update computeMatrix wrapper

* Decrease memory needs (#817)

* Use an iterator to not blow memory up

* Update a bit more

* The GC bias stuff is all deprecated, I'm not fixing that old code

* Cache resulting counts rather than just decreasing the bin size (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #816

* expose option

* Add a test using pseudocounts and skipZeroOverZero

* syntax

* Fix tests

* Make --skipZeroOverZero a galaxy macro and add to bigwigCompare

* [ci skip] a bit of formatting

* Fix #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* Fix python version

* Update azure-pipelines.yml

* fixed typo (#864)

* Develop (#827)

* Merged into the wrong branch without noticing :( (#814)

* use better conda link (#799)

* Estimated filtering fix (#813)

* oops

* fix testing and set a max number of filtered reads

* apparently a bunch of things were getting skipped

* fix wrappers

* update computeMatrix wrapper

* Decrease memory needs (#817)

* Use an iterator to not blow memory up

* Update a bit more

* The GC bias stuff is all deprecated, I'm not fixing that old code

* Cache resulting counts rather than just decreasing the bin size (#818)

* Cache resulting counts rather than just decreasing the bin size

* sanity check

* Implement #815

* [skip ci] update change log

* Implement #816 (#825)

* Implement #816

* expose option

* Add a test using pseudocounts and skipZeroOverZero

* syntax

* Fix tests

* Make --skipZeroOverZero a galaxy macro and add to bigwigCompare

* [ci skip] a bit of formatting

* Fix #822 (#826)

* fixes linting issues (#837)

* Delete #test.bg# (#859)

File is removed upon clean.

* fixed typo

* Update test images, skip testing if the wrong matplotlib version is used (#865)

* Update test images, skip testing if the wrong matplotlib version is used

* Update test-template.yml

* linting

* can't conda activate on azure

* now the heatmap is correct and the profile is wrong

* lint

* only one test should fail now

* Fix #844

* Should fix one test at least

* fix last tests

* fix #838 (#843)

* fix #838

* fixes

* Update CHANGES.txt

* Close #868 #867 and #851 (#869)

* Fix #868

* Fix #867

* Default ALL the things!

* Fix #866 (#871)

* release 3.3.1

* try github actions

* each action is a file

* OK, that's inflexible

* OK, the action.yml thing is a mess

* syntax

* ok, try this

* uses

* spacing

* ok

* do anchors work?

* boo, so duplicative!

* oops

* maybe this will work for pypi

* ensure dist is empty

* nev

* rename

* bump version number
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docs Release 3.3.1 (#872) Sep 10, 2019
galaxy Release 3.3.1 (#872) Sep 10, 2019
gallery Merge branch 'master' of https://github.com/fidelram/deepTools into m… Oct 29, 2014
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.gitignore [ci skip] Don't ignore deeptools/_version.py Aug 21, 2018
.planemo.sh Azure pipelines (#804) Feb 14, 2019
CHANGES.txt Release 3.3.1 (#872) Sep 10, 2019
LICENSE.txt while I'm at it; assuming those don't need to be executable either Feb 8, 2016
MANIFEST.in dti is a dependency now (#781) Nov 17, 2018
README.md Azure pipelines (#804) Feb 14, 2019
README.rst fix #498 Mar 28, 2017
azure-pipelines.yml Release 3.3.1 (#872) Sep 10, 2019
requirements.txt Release 3.3.1 (#872) Sep 10, 2019
setup.py Release 3.3.1 (#872) Sep 10, 2019

README.md

deepTools

Build Status Documentation Status PyPI Version install with bioconda

User-friendly tools for exploring deep-sequencing data

deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.

For support, questions, or feature requests contact: deeptools@googlegroups.com

Citation:

Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research. 2016 Apr 13:gkw257.

Documentation:

Our documentation contains more details on the individual tool scopes and usages and an introduction to our deepTools Galaxy web server including step-by-step protocols.

Please see also the FAQ, which we update regularly. Our Gallery may give you some more ideas about the scope of deepTools.

For more specific troubleshooting, feedback, and tool suggestions, contact us via deeptools@googlegroups.com.


Installation

deepTools are available for:

  • Command line usage (via pip/anaconda/github)
  • Integration into Galaxy servers (via toolshed/API/web-browser)

There are many easy ways to install deepTools. Details can be found here

Install by cloning this repository:

You can install any one of the deepTools branches on command line (linux/mac) by cloning this git repository :

$ git clone https://github.com/deeptools/deepTools
$ cd deepTools
$ python setup.py install

By default, the script will install the python library and executable codes globally, which means you need to be root or administrator of the machine to complete the installation. If you need to provide a nonstandard install prefix, or any other nonstandard options, you can provide many command line options to the install script.

$ python setup.py --help

For example, to install under a specific location use:

$ python setup.py install --prefix <target directory>

To install into your home directory, use:

$ python setup.py install --user

Galaxy Installation

deepTools can be easily integrated into Galaxy. Please see the installation instructions in our documentation for further details.

Note: From version 2.3 onwards, deepTools support python3. In case of any problems running with python3/python2, contact our user group : deeptools@googlegroups.com.


This tool suite is developed by the Bioinformatics Facility at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.

Documentation | deepTools Galaxy | FAQ

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