What is a Bioconductor package?

What is a Bioconductor package?

Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. The use of these packages provides a basic understanding of the R programming / command language.

What is limma voom?

voom is a function in the limma package that modifies RNA-Seq data for use with limma. Together they allow fast, flexible, and powerful analyses of RNA-Seq data.

What is Limma trend?

limma-trend is useful for processing expression values that show a mean-variance relationship. This is often useful for microarray data, and it can also be applied to RNA-seq counts that have been converted to log2-counts per million (logCPM) values (Law et al, 2014).

What can you do with Bioconductor?

Bioconductor provides access to powerful statistical and graphical methods for the analysis of genomic data. It also facilitates the integration of biological metadata like GenBank, GO, LocusLink and PubMed in the analysis of experimental data.

How many Bioconductor packages are there?

Bioconductor is a collection of open-source tools that use R. It contains over 1400 R packages that can be used to analyze many types of biological data.

Does edgeR use Limma?

Both the edgeR and limma gene set test methods call the same underlying test functions, the only difference is in how the counts are transformed at the beginning. The edgeR methods use a transformation based on the fitted negative binomial model, which is obviously not relevant for a limma analysis.

What is Limma precision?

The limma pipeline includes linear modeling to analyze complex experiments with multiple treatment factors, quantitative weights to account for variations in precision between different observations, and empirical Bayes statistical methods to borrow strength between genes.

Is Bioconductor useful?

Why are packages removed from Bioconductor?

The warning is emitted when the package is loaded, and is reported on the package ‘landing page’. The message alerts users that the package currently fails the minimal build and check criteria, and that the package will likely be removed from Bioconductor in the next release.