.. main file for htsint documentation htsint ===================================================== .. figure:: ../figures/example-web.png :scale: 55% :align: center :alt: example functional module :figclass: align-center ------- ``htsint`` (High-Throughput Sequencing INTegrate) is a Python package used to create gene sets for the study of high-throughput sequencing data. The goal is to create functional modules through the integration of heterogeneous types of data. These functional modules are primarily based on the Gene Ontology [Ashburner00]_, but as the package matures additional sources of data will be incorporated. The functional modules produced can be subsequently tested for significance in terms of differential expression in RNA-Seq or microarray studies using gene set enrichment analysis [Subramian05]_. Shown below is the placement of ``htsint`` in an example analysis pipeline. .. figure:: ../figures/figure-conceptual.png :scale: 65% :align: center :alt: example RNA-Seq pipeline :figclass: align-center Who are the intended users? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The software in its current form is an API library and because HTS pipelines have different goals with many varied tasks required to achieve these goals, a flexible library in a scripting language commonly used in bioinformatics was selected. The target audience for ``htsint`` are developers that piece together high-throughput sequencing (HTS) pipelines. That being said one important aspect of this project is to provide both abstracted functions for non-Python programmers as well as convenient means to enable high levels of customization. Features ^^^^^^^^^^^^^^ 1. The data are locally stored and maintained in a :doc:`database ` 2. The database is fully accessible and modifiable through `SQLAlchemy `_. 3. Visualization tools like heatmaps and interaction networks included 4. The user has complete control over the information used to generate gene sets 5. Easy to follow examples that require only a basic knowledge of Python General contents: ----------------------- .. toctree:: :maxdepth: 1 install database Tutorials: --------------------- .. toctree:: :maxdepth: 1 Database cookbook Using BLAST Gene Ontology annotation fetching Gene level differential expression Gene set analysis example Pathway example References Citation ^^^^^^^^^^^^ If you find ``htsint`` useful for your research or if you want to learn more about the software please refer to the following publication. A. J. Richards, A Herrel, & C. Bonneaud. `htsint: a Python library for sequencing pipelines that combines data through gene set generation `_. **BMC Bioinformatics**, 2015, 16, 307