From f5906f2c4e5c9391487c8256a19cc98e9dafc804 Mon Sep 17 00:00:00 2001 From: Annika Fust Date: Mon, 14 Nov 2016 14:18:03 +0100 Subject: [PATCH] pdf version update --- docs/index.md | 39 ++++++++++++++++++++++++++++++++++++++- docs_rst/index.rst | 6 +++--- docs_rst/output-pdf.rst | 8 ++------ docs_rst/output.rst | 8 ++------ mkdocs.yml | 9 --------- 5 files changed, 45 insertions(+), 25 deletions(-) diff --git a/docs/index.md b/docs/index.md index 2fce14c..c184a2d 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,3 +1,40 @@ **Welcome to the UROPA documentation!** -Please visit the [UROPA-manual](http://uropa-manual.readthedocs.io/en/latest/) \ No newline at end of file +UROPA is a command line based tool, intended for genomic region annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. +These can be sensitive for feature type, distance, strand specificity, feature attributes (eg. protein_coding) or the anchor position relative to the feature. +UROPA can incorporate reference annotation files (GTF) from different sources, like Gencode, Ensembl, or RefSeq, as well as custom reference files produced by the user. + +**Advantages of UROPA** + +* Simple usage: No programming +* Utilization of all available GTF files as annotation database +* Detect the most appropriate annotation with flexible keys that allow robustness and simple customization, such as + * feature type + * feature anchor + * feature direction relative to peak location + * filter for attribute values, e.g. "protein_coding" + * strand specificity +* Preparation of custom annotation files +* One run with multiple sets of parameters by multiple queries +* Graduated annotation due to priorization +* Different easily-readable output tables (AllHits, FinalHits, BestperQuery_Hits). +* Visual summary for annotation evaluation +* Annotation with default values + +**How to cite** + +Please cite the paper describing UROPA when using it in your research: +tba + +**Contribute** + +Source Code [here](https://github.molgen.mpg.de/loosolab/UROPA) +Further details see [here](http://uropa.readthedocs.io/en/latest/install/) + +**Support** + +If you have any issue feel free to send an email to Maria Kondili (maria.kondili@mpi-bn.mpg.de) + +**Licence** + +The project is licensed under the MIT license diff --git a/docs_rst/index.rst b/docs_rst/index.rst index 1bffe2c..05bf18e 100644 --- a/docs_rst/index.rst +++ b/docs_rst/index.rst @@ -59,9 +59,9 @@ The project is licensed under the MIT license (see :doc:`/license`) install parameter config - output - uropa-example - custom + output-pdf + uropa-example-pdf + custom-pdf license help \ No newline at end of file diff --git a/docs_rst/output-pdf.rst b/docs_rst/output-pdf.rst index 4abbf54..d48415e 100644 --- a/docs_rst/output-pdf.rst +++ b/docs_rst/output-pdf.rst @@ -17,12 +17,8 @@ File overview - **Uropa_Summary**: Statistical summary of the UROPA annotation by using the ``-s`` parameter. .. note:: - The output files will be named additionally by the output directory name. - For example if uropa is used like this: - - .. code:: bash - - uropa -i config.json -o ChIPanno + The output files will be named additionally by the output directory name. + For example if uropa is used like this: ``uropa.py -i config.json -o ChIPanno`` The result would contain: ChIPannot/Uropa_AllHits_ChIPannot.txt diff --git a/docs_rst/output.rst b/docs_rst/output.rst index c3a1ff8..973021f 100644 --- a/docs_rst/output.rst +++ b/docs_rst/output.rst @@ -17,12 +17,8 @@ File overview - **Uropa_Summary**: Statistical summary of the UROPA annotation by using the ``-s`` parameter. .. note:: - The output files will be named additionally by the output directory name. - For example if uropa is used like this: - - .. code:: bash - - uropa.py -i config.json -o ChIPanno + The output files will be named additionally by the output directory name. + For example if uropa is used like this: ``uropa.py -i config.json -o ChIPanno`` The result would contain: ChIPannot/Uropa_AllHits_ChIPannot.txt diff --git a/mkdocs.yml b/mkdocs.yml index b4f1888..83993d5 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -5,12 +5,3 @@ repo_url: 'https://github.molgen.mpg.de/loosolab/UROPA' repo_name: 'GitHub' pages: - Home: 'index.md' -- About UROPA: 'introduction.md' -- Installation: 'install.md' -- Available parameters: 'parameters.md' -- Configuration file: 'config.md' -- Output: 'output.md' -- Application examples: 'uropa-example.md' -- Side tool - 'UROPA to GTF': custom.md -- MIT License: license.md -- Help: help.md