binary-only release

1.2.0-binary

Dummy commit to test github integration.

1.2.0

Simplified dependencies to make it installable with bioconda. Added clusterProfiler with functions to do pathway analysis. Added support for sleuth.

v1.1.1

Echos the progress of the R script run. Also adds more useful failure messages when all of the necessary R libraries are not installed.

v1.1.0

Updates bcbio.rnaseq to use transcript level counts from Sailfish, using Mike Love's tximport library. Adds searchable, sortable tables via the datatables R package.

v1.0.4

Adds initial support for Sleuth and handling of bcbio-nextgen runs where Qualimap rnaseq could not run.

v1.0.3

Preparing for installation via bioconda

Adds a --version flag for post-installation sanity checking.

v1.0.2

Bug fix: Call biomaRt with a specific backup server to avoid server problems.

v1.0.1

Tagging this release to get bcbio-rnaseq added to bcbio-nextgen proper.

Release 1.0

First release supporting:

1. comparison of R and non-R based RNA-seq DE callers
2. summary reports of bcbio-nextgen RNA-seq runs
3. SEQC comparisons for benchmarking bcbio-nextgen RNA-seq pipeline changes

Initial pre-release.

• When run with a SEQC dataset compares to the ~ 1000 genes abundances calculated via RT-PCR in the SEQC experiment
• ERCC analyses are detected automatically and run
• Output of a bcbio-nextgen run can be used to do a single factor analysis of a RNA-seq experiment