Commit cdd2db3a authored by Christian Arnold's avatar Christian Arnold

Bugfix for plotting circular plot, documentation test and update for ReadTheDocs

parent c590f1ce
,carnold,carnold,30.11.2017 14:57,file:///home/carnold/.config/libreoffice/4;
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.. _docs-quickstart:
============================================================
Try it out now!
============================================================
The following quick start briefly summarizes the necessary steps to use our pipeline:
1. Install the necessary tools (Snakemake, samtools, bedtools, and Subread). We recommend installing them via conda, in which case the installation is as easy as
``conda install -c bioconda snakemake bedtools samtools subread``
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. If you want to install the tools manually and outside of the conda framework, see the following instructions for each of the tools: `snakemake <http://snakemake.readthedocs.io/en/stable/getting_started/installation.html>`_, `samtools <http://www.htslib.org/download>`_, `bedtools <http://bedtools.readthedocs.io/en/latest/content/installation.html>`_, `Subread <http://subread.sourceforge.net>`_.
2. Clone the Git repository:
``git clone https://git.embl.de/grp-zaugg/diffTF``
3. To run the example analysis for 50 TF, simply perform the following steps:
* Change into the ``example/input`` directory within the Git repository
``cd diffTF/example/input``
* Download the data via the download script
``sh downloadAllData.sh``
* To test if the setup is correct, start a dryrun via the first helper script
``sh startAnalysisDryRun.sh``
* Once the dryrun is successful, start the analysis via the second helper script
``sh startAnalysis.sh``
4. To run your own analysis, modify the files ``config.json`` and ``sampleData.ts``. See the instructions in the section `Run your own analysis`_ for more details.
5. If your analysis finished successfully, take a look into the ``FINAL_OUTPUT`` folder within your specified output directory, which contains the summary tables and visualization of your analysis. If you received an error, take a look in Section :ref:`docs-errors` to troubleshoot.
.. _docs-prerequisites:
============================================================
Prerequisites
============================================================
This section lists the required software and how to install them. As outlined in Section :ref:`docs-quickstart`, the easiest way is to install all of them via ``conda``. However, it is of course also possible to install the tools separately.
--------------------------
Snakemake
--------------------------
Please ensure that you have at least version 4.3 installed. Principally, there are `multiple ways to install Snakemake <http://snakemake.readthedocs.io/en/stable/getting_started/installation.html>`_. We recommend installing it, along with all the other required software, via conda.
----------------------------
samtools, bedtools, Subread
----------------------------
In addition, `samtools <http://www.htslib.org/download>`_, `bedtools <http://bedtools.readthedocs.io>`_ and `Subread <http://subread.sourceforge.net>`_ are needed to run *diffTF*. We recommend installing them, along with all the other required software, via conda.
--------------------------
R and R packages
--------------------------
A working ``R`` installation is needed and a number of packages from either CRAN or Bioconductor have to be installed. Type the following in ``R`` to install them:
.. code-block:: R
install.packages(c("checkmate", "futile.logger", "tidyverse", "reshape2", "gridExtra", "scales", "jsonlite", "RcolorBrewer", "rlist", "ggrepel", "lsr", "modeest", "locfdr", "boot"))
source("https://bioconductor.org/biocLite.R")
biocLite(c("limma", "vsn", "csaw", "DESeq2", "DiffBind", "geneplotter", "Rsamtools"))
.. _docs-runOwnAnalysis:
============================================================
Run your own analysis
============================================================
.. _docs-details:
============================================================
Workflow
============================================================
============================================================
Input
============================================================
============================================================
Output
============================================================
============================================================
Working with the pipeline
============================================================
.. _docs-errors:
============================================================
Handling errors
============================================================
.. _docs-details:
Input
======
Workflow
=========
Working with the pipeline
=========================
Handling errors
===============
Output
======
......@@ -3,18 +3,37 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to diffTF's documentation!
==================================
=========================================
Welcome to the documentation of *diffTF*!
=========================================
Welcome to the *diffTF* documentation, and thank you for the interest in our software! These pages provide documentation and additional information for the *diffTF* pipeline.
To get yourself oriented, check the menu on the left or search what you are looking for in the search field in the upper left corner.
This site is organized into the following three parts:
.. toctree::
:maxdepth: 2
:caption: Contents:
.. toctree::
:maxdepth: 2
:caption: Quick Start and Installation
Indices and tables
==================
chapter1.rst
.. toctree::
:maxdepth: 2
:caption: Pipeline Details
chapter2.rst
.. toctree::
:maxdepth: 2
:caption: Project Information
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
projectInfo.rst
.. _docs-project:
Biological motivation
============================
Transcription factor (TF) activity constitutes an important readout of cellular signalling pathways and thus for assessing regulatory differences across conditions. However, current technologies lack the ability to simultaneously assessing activity changes for multiple TFs and surprisingly little is known about whether a TF acts as repressor or activator. To this end, we introduce the widely applicable genome-wide method diffTF to assess differential TF binding activity and classifying TFs as activator or repressor by integrating any type of genome-wide chromatin with RNA-Seq data and in-silico predicted TF binding sites
Help, contribute and contact
============================
If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation. For method-related questions, contact Judith B. Zaugg (judith.zaugg@embl.de) or Ivan Berest (berest@embl.de). For technical questions, contact Christian Arnold (christian.arnold@embl.de).
If you have questions, doubts, ideas or problems, please use the Issue Tracker at https://git.embl.de/grp-zaugg/diffTF/issues. We will respond in a timely manner.
Citation
================
If you use this software, please cite the following reference:
Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. Genome-wide quantification of differential transcription factor activity: diffTF. 2017. submitted.
Frequently asked questions
=============
Change log
==========================
License
============================
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