SOFTWARE

USER MANUAL

icon_book_11
DOWNLOAD USER GUIDE 
(v1.2.3)

The user’s manual is a practical reference for analysing sequins with Anaquin. Where possible, we have described the use and analysis of sequins in the context of real-life experimental scenarios. The manual also provides step-by-step tutorials, example outputs, usage options and other useful information.


USAGE & OPTIONS

icon_usage_3

COMMAND LINE & R TOOL OPTIONS

Anaquin includes a range of tools to help analyse sequins in a next-generation sequencing library. Please find below a list of the available tools in both command line and R programming environments, with a brief description of applications, optional arguments, example output results and other useful information.

TOOL (C++) DESCRIPTION
RnaAlign Measure spliced read alignments from sequins on the in silico chromosome.
RnaAssembly Compares assembled transcript models to sequin annotations in the in silico chromosome.
RnaExpression Quantitative analysis of sequin expression.
RnaFoldChange Assess fold-changes in sequin expression between multiple samples.
RnaSubsample Calibrate sequence coverage of sequins across multiple replicates.
TOOL (R) DESCRIPTION
AnaquinData Create an Anaquin dataset. The resulting R-object is required for every Anaquin analysis.
PlotLinear Plot linear model between measured and observed abundance of sequins.
PlotLogistic Plot logistic model of assembly sensitivity against measured abundance for sequins.
PlotROC Plot a receiver operating characteristic (ROC) curve that models true positive rate to false positive rate detection.
PlotLODR Create a Limit-of-Detection Ratio (LODR) plot between measured abundance and confidence (p-value)

DOWNLOAD

icon_install_4 DOWNLOAD ANAQUIN
(beta v1.1)

Download the latest version (beta v1.1) of the Anaquin software toolkit, and be sure to update your version regularly to benefit from the latest bug fixes and improvements. Please note that this is a beta release and Anaquin is under active development, and you may be occasionally confronted with bugs we have not yet caught. If this happens to you, please send an email including the command line and error message (if required, we may request some sample data) to anaquin@garvan.org.au or open a ticket issue on our GitHub repository – github.com/student-t/Anaquin

Version history is available here.


INSTALL

icon_install_2

COMPILE FROM SOURCE

Anaquin is C++ 0x11 software. To build the software from source, you will need the following dependencies: (1) Eigen (http://eigen.tuxfamily.org(2) Catch (https://github.com/philsquared/Catch) (3) KLib (https://github.com/attractivechaos/klib) (4) Boost (http://www.boost.org/users/download).

Once the dependencies are installed, run make to build the software. The code requires a C++ 0x11 compiler. We have tested the compilation with g++ and xCode, however, other compilers might also work (Windows is not currently supported). To test your installation, run version check.

$ anaquin –v

INSTALL R PACKAGE

To install Anaquin for the Bioconductor, follow the instructions at https://bioconductor.org/packages/devel/bioc/html/Anaquin.html.

SOURCE CODE & LICENSE

Anaquin is freely available under BSD license. Source code is available at GitHub – www.github.com/student-t/Anaquin.

garvan_greyGarvan Institute of Medical Research © 2016 / All rights reserved / LEGAL