Commit 5c7e6458 authored by Christian Arnold's avatar Christian Arnold

Documentation updates

parent 21fb4f25
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Try it out now!
============================================================
The following quick start briefly summarizes the necessary steps to use our pipeline:
diffTF runs on Linux and macOS. The following quick start briefly summarizes the necessary steps to use our pipeline:
1. Install the necessary tools (*Snakemake*, *samtools*, *bedtools*, and *Subread*).
.. note:: Note that all tools require Python 3.
We recommend installing them via conda, in which case the installation is as easy as
We recommend installing them via conda, in which case the installation then becomes as easy as
.. code-block:: Bash
conda install -c bioconda snakemake bedtools samtools subread
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install snakemake bedtools samtools subread
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. Installation is quick and easy.
If conda is not yet installed, follow the `installation instructions <https://conda.io/docs/user-guide/install/index.html>`_. Installation is quick and easy. Make sure to open a new terminal after installation, so that *conda* is available.
.. note:: You do not need to uninstall other Python installations or packages in order to use conda. Even if you already have a system Python, another Python installation from a source such as the macOS Homebrew package manager and globally installed packages from pip such as pandas and NumPy, you do not need to uninstall, remove, or change any of them before using conda.
......@@ -27,6 +30,20 @@ The following quick start briefly summarizes the necessary steps to use our pipe
git clone https://git.embl.de/grp-zaugg/diffTF
If you receive an error, *Git* may not be installed on your system. If you run Ubuntu, try the following command:
.. code-block:: Bash
sudo apt-get install git
For macOS, there are multiple ways of installing it. If you already have *Homebrew* (http://brew.sh) installed, simply type:
.. code-block:: Bash
brew install git
Otherwise, consult the internet on how to best install Git for your system.
3. To run the example analysis for 50 TF, simply perform the following steps:
* Change into the ``example/input`` directory within the Git repository
......@@ -68,7 +85,7 @@ 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*, *bedtool*s, *Subread*
*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.
......@@ -81,11 +98,10 @@ A working ``R`` installation is needed and a number of packages from either CRAN
.. code-block:: R
install.packages(c("checkmate", "futile.logger", "tidyverse", "reshape2", "gridExtra", "scales", "jsonlite", "RcolorBrewer", "rlist", "ggrepel", "lsr", "modeest", "locfdr", "boot"))
install.packages(c("checkmate", "futile.logger", "tidyverse", "reshape2", "RColorBrewer", "ggrepel", "lsr", "modeest", "boot", "grDevices", "pheatmap", "matrixStats", "locfdr"))
source("https://bioconductor.org/biocLite.R")
biocLite(c("limma", "vsn", "csaw", "DESeq2", "DiffBind", "geneplotter", "Rsamtools"))
.. _docs-runOwnAnalysis:
......@@ -98,4 +114,4 @@ Running your own analysis is almost as easy as running the example analysis. Car
2. Modify the file ``config.json`` accordingly. For example, we strongly recommend running the analysis for all TF instead of just 50 as for the example analysis. For this, simply change the parameter “TFs” to “all”. See Section :ref:`configurationFile` for details about the meaning of the parameters. Do not delete or rename any parameters or sections.
3. Create a tab-separated file that defines the input data, in analogy to the file ``sampleData.tsv`` from the example analysis, and refer to that in the file ``config.json`` (parameter ``summaryFile``)
4. Adapt the file ``startAnalysis.sh`` if necessary (the exact command line call to Snakemake and the various Snakemake-related parameters)
5. Since running the pipeline might be computationally demanding, read Section :ref:`timeMemoryRequirements` and decide on which machine to run the pipeline. In most cases, we recommend running *diffTF* in a cluster environment. The pipeline is written in Snakemake, and we strongly suggest to also read Section :ref:`workingWithPipeline` to get a basic understanding of how the pipeline works.
5. Since running the pipeline is often computationally demanding, read Section :ref:`timeMemoryRequirements` and decide on which machine to run the pipeline. In most cases, we recommend running *diffTF* in a cluster environment (see Section :ref:`clusterEnvironment` for details). The pipeline is written in Snakemake, and we strongly suggest to also read Section :ref:`workingWithPipeline` to get a basic understanding of how the pipeline works.
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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
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.
For a graphical summary of the idea, see the section :ref:`workflow`
Help, contribute and contact
============================
......@@ -16,7 +19,7 @@ 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.
Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Giovanni Palla, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. *Genome-wide quantification of differential transcription factor activity: diffTF*. 2018. submitted.
Change log
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<li class="toctree-l1"><a class="reference internal" href="chapter1.html">Try it out now!</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter1.html#prerequisites">Prerequisites</a><ul>
<li class="toctree-l2"><a class="reference internal" href="chapter1.html#id1">Snakemake</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter1.html#samtools-bedtool-s-subread"><em>samtools</em>, <em>bedtool*s, *Subread</em></a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter1.html#samtools-bedtools-subread"><em>samtools</em>, <em>bedtools</em>, <em>Subread</em></a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter1.html#r-and-r-packages">R and R packages</a></li>
</ul>
</li>
......@@ -212,6 +212,7 @@
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-difftf-and-faqs">Working with <em>diffTF</em> and FAQs</a><ul>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#general-remarks">General remarks</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#executing-difftf-running-times-and-memory-requirements">Executing diffTF - Running times and memory requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#running-difftf-in-a-cluster-environment">Running <em>diffTF</em> in a cluster environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="chapter2.html#frequently-asked-questions">Frequently asked questions</a></li>
</ul>
</li>
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<li class="toctree-l1"><a class="reference internal" href="chapter2.html">Workflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#input">Input</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#output">Output</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-the-pipeline-and-frequently-asked-questions">Working with the pipeline and frequently asked questions</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#working-with-difftf-and-faqs">Working with <em>diffTF</em> and FAQs</a></li>
<li class="toctree-l1"><a class="reference internal" href="chapter2.html#handling-errors">Handling errors</a></li>
</ul>
<p class="caption"><span class="caption-text">Project Information</span></p>
......@@ -175,7 +175,8 @@
<div class="section" id="biological-motivation">
<span id="docs-project"></span><h1>Biological motivation<a class="headerlink" href="#biological-motivation" title="Permalink to this headline"></a></h1>
<p>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</p>
<p>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.</p>
<p>For a graphical summary of the idea, see the section <a class="reference internal" href="chapter2.html#workflow"><span class="std std-ref">Workflow</span></a></p>
</div>
<div class="section" id="help-contribute-and-contact">
<h1>Help, contribute and contact<a class="headerlink" href="#help-contribute-and-contact" title="Permalink to this headline"></a></h1>
......@@ -185,7 +186,7 @@
<div class="section" id="citation">
<h1>Citation<a class="headerlink" href="#citation" title="Permalink to this headline"></a></h1>
<p>If you use this software, please cite the following reference:</p>
<p>Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin &amp; Judith B. Zaugg. <em>Genome-wide quantification of differential transcription factor activity: diffTF</em>. 2017. submitted.</p>
<p>Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Giovanni Palla, Kasper Dindler Rassmussen, Kristian Helin &amp; Judith B. Zaugg. <em>Genome-wide quantification of differential transcription factor activity: diffTF</em>. 2018. submitted.</p>
</div>
<div class="section" id="change-log">
<h1>Change log<a class="headerlink" href="#change-log" title="Permalink to this headline"></a></h1>
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"conditionComparison": "GMP,MPP",
"designContrast": "~ conditionSummary",
"designVariableTypes": "conditionSummary:factor",
"nPermutations": 5,
"nPermutations": 70,
"nBootstraps": 0,
"nCGBins": 10,
"TFs": "CTCF,CEBPB,SNAI2,CEBPA,UBIP1,CEBPG,CEBPD,ZFX,AP2D,PAX5.S,SNAI1,ZEB1,SP4,MBD2,IRF1,MECP2,PAX5.D,SP3,NFIA.C,SP1.A,IRF7,MYF6, NRF1,DBP,MAZ,NKX28,DLX2,GATA1,P53,ZN143,AIRE,NR2C2,HMGA1,FUBP1,TEAD3,OVOL1,HXD4,KLF1,RXRG,HNF1B,ZIC3,HNF1A,NANOG.S,GFI1,PO3F1,NR2C1,ELF5,TF65.C,NFAC3,TEAD1",
......
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