April 25, 2017

Bioconductors:

We are pleased to announce Bioconductor 3.5, consisting of 1383
software packages, 316 experiment data packages, and 911 annotation
packages.

There are 88 new software packages, and many updates and improvements
to existing packages; Bioconductor 3.5 is compatible with R 3.4,
and is supported on Linux, 32- and 64-bit Windows, and Mac OS X.  This
release will include an updated Bioconductor [Amazon Machine Image][1]
and [Docker containers][2].

Visit [https://bioconductor.org][3]
for details and downloads.

[1]: https://bioconductor.org/help/bioconductor-cloud-ami/
[2]: https://bioconductor.org/help/docker/
[3]: https://bioconductor.org

Contents
--------

* [Getting Started with Bioconductor
3.5](#getting-started-with-bioconductor-35)
* [New Software Packages](#new-software-packages)
* [NEWS from new and existing
packages](#news-from-new-and-existing-packages)
* [Deprecated and Defunct Packages](#deprecated-and-defunct-packages)

Getting Started with Bioconductor 3.5
======================================

To update to or install Bioconductor 3.5:

1. Install R 3.4.  Bioconductor 3.5 has been designed expressly for
   this version of R.

2. Follow the instructions at
   [http://bioconductor.org/install/](http://bioconductor.org/install/).

New Software Packages
=====================

There are 88 new software packages in this release of Bioconductor. For
full details see the official release link below.

NEWS from new and existing packages
===================================

There is too much NEWS to include here, see the full release
announcement at

   https://bioconductor.org/news/bioc_3_5_release/

Deprecated and Defunct Packages
====================================

​One software package (betr) was removed from this release (after being

deprecated in BioC 3.4).

Nine software packages (AtlasRDF, coRNAi, saps, MeSHSim, GENE.E, mmnet,
CopyNumber450k, GEOsearch, pdmclass) are deprecated in this release and
will be removed in BioC 3.6.

Two experimental data packages (encoDnaseI, ggtut) were removed from this
release (after being deprecated in BioC 3.4).

One experimental data package (CopyNumber450kData) is deprecated in this
release and will be removed in BioC 3.6.