ROGER

Understand gene expression regulation with ROGER (Roche Omnibus of Gene Expression Regulation)

Software requirements

Python 3 or greater

Instalaltion

Install Python 3 (https://www.python.org/downloads/) on your system or create an virtual environment
Clone this repository to your preferred ROGER installation directory

git clone git@github.com:bedapub/roger.git

Switch to the cloned root directory of ROGER and install ROGER through pip:

pip install -e .

Create a configuration file called .roger_config.cfg in your user home directory and add your SQLAlchemy property there. An example configuration file could look like this:

# http://docs.sqlalchemy.org/en/latest/core/engines.html
SQLALCHEMY_DATABASE_URI="sqlite:///roger-schema.db"
ROGER_DATA_FOLDER="some_folder" #default is /tmp or other temporary directory

Initialize ROGER with the following command:

roger init

Populate ROGER with additional data by using its command line interface. See setup_example.sh for more information
Install additional R packages:
1. ribiosROGER, ribiosIO and ribiosExpression from RIBIOS
2. Bioconductor and the limma package.

Adding annotation support for other species

After installation, ROGER can only consume expression data from human. You can use the add-species command add support for other species in ROGER. For example, the following commands:

roger add-species "rnorvegicus_gene_ensembl" 10116
roger add-species "mmusculus_gene_ensembl" 10090

Would enable ROGER to consume data from rat and mouse as well. Internaly, ROGER will downlaod gene identifiers from the Ensembl BioMart service and assign them with internal identifiers to allow efficient indexing.

Example DGE & GSE analysis

Every data set used for the following examples can be found in test_data.

DGE Analysis with microarray data / limma:

Create a new microarray dataset:
```
roger add-ds-ma test_data/ds/ma-example-signals.gct 10090 affy_mouse430_2
```
This will add the normalized expression matrix "ma-example-signals.gct" to the database. ROGER will automatically annotate the feature names inside the expression matrix based on the given taxon id (here mouse) and feature symbol type (here AFFY Mouse430A 2 prope set). Additionally, ROGER will use the GCT file name as study name if nothing else is specified by parameter --name. You can use roger show-symbol-types 10090 to see a list of supported feature types / probe sets
Add a design matrix
```
roger add-design "test_data/ds/ma-example-design.txt" ma-example-signals
```
Use roger remove-design ma-example-design ma-example-signals to remove the design matrix from ma-example-signals

Add a contrast matrix

roger add-contrast test_data/ds/ma-example-contrast.txt ma-example-design ma-example-signals

Execute limma on added data set:

roger run-dge-ma ma-example-contrast ma-example-design ma-example-signals

Execute CAMERA for limma:

roger run-gse ma-example-contrast ma-example-design ma-example-signals limma

Export results to files:

roger export-dge-table ma-example-contrast ma-example-design ma-example-signals limma output.txt
roger export-gse-table ma-example-contrast ma-example-design ma-example-signals limma CAMERA output.txt

DGE Analysis with RNAseq data / edgeR:

The DGE analysis for RNAseq data works similar compared to the DGE analysis for microarray data. Only the commands for importing data sets and running the DGE analysis are different, because these commands provide slightly different optional parameters

roger add-ds-rnaseq test_data/ds/rnaseq-example-readCounts.gct 9606 entrezgene
roger add-design test_data/ds/rnaseq-example-DesignMatrix.txt rnaseq-example-readCounts
roger add-contrast test_data/ds/rnaseq-example-ContrastMatrix.txt rnaseq-example-DesignMatrix rnaseq-example-readCounts
roger run-dge-rnaseq rnaseq-example-ContrastMatrix rnaseq-example-DesignMatrix rnaseq-example-readCounts
roger run-gse rnaseq-example-ContrastMatrix rnaseq-example-DesignMatrix rnaseq-example-readCounts edgeR

Other Commands

Use roger --help to get a more detailed description of all available roger commands

bedapub/roger