Datasets packaged with the software that produced them, and sometimes also with software that facilitates access to or analysis of the data.
Dynamic algorithms for resource provisioning and job allocation suitable for the chosen dataset are packaged and delivered in a privileged virtual machine as part of the container.
To rectify this, we have now prepared the scripts used to produce the results in this manuscript for public release on our lab wiki (the corresponding link: http://tmpl.arizona.edu/dokuwiki/doku.php?id=bioinformatics:scripts:vsb) and a GitHub repository (https://github.com/simroux/virsorter-curated-dataset-scripts-package).
To quantitatively assess performance, we manually segmented nuclei in two different regions of adjacent time points in the Drosophila dataset using the software package Imaris (Bitflow).
This created a numerical profile which was analysed as a character dataset using Bionumerics software package version 3.5 (Applied-Maths, Sint-Martens-Latern, Belgium).
While the estimated binding signal is of good utility and can be conveniently computed for a given dataset using our software package, by extension, we can envision a complete ChIP-seq analysis methodology where the raw ChIP-seq signal would be subjected to a comprehensive multistage decomposition process, taking into account all relevant control datasets at the same time.
Briefly, cell lines selected from the NCI-60 for the Affymetrix HG-U95 based Av2 predictors[4] were used in the HG-U133A-based docetaxel and etoposide predictors, multiple t-tests were applied on the dataset using statistical package R (version 2.5.1), and the binary regression parameters were adjusted to achieve optimal cross-validation accuracy.
To illustrate Confero platform functionality we walk through major aspects of the Confero workflow and results using the Bioconductor estrogen package dataset.
False discovery analysis was then applied to the dataset using r package ' q value' (v 1.30.0, Dabney, A and Storey, J).
We compared the one-ratio model with the free-ratio model to test the lineage-specific positive selection for the PL10 related functional homologs in our dataset using PAML4 package [ 20].
