[Bioc-devel] ANN: Bioconductor Release 1.7 is available

Seth Falcon sfalcon at fhcrc.org
Sat Oct 15 01:56:16 CEST 2005

We are pleased to announce the release of Bioconductor 1.7.  This
release includes 17 new packages and many improvements and bug fixes
to existing packages.

Please visit http://www.bioconductor.org for details and downloads.


- Release Highlights
- Getting Started With Bioconductor 1.7
- Known Issues
- 17 New Packages

Release Highlights

- Rgraphviz is now available as a binary package for Windows

- Annotation data packages now include protein information from IPI
  (see the PFAM and PROSITE environments in the data packages).

Getting Started With Bioconductor 1.7

To get started with Bioconductor 1.7, please:

- Install R 2.2.0.  Bioconductor 1.7 has been designed expressly for
  this version of R.

- Follow the instructions here:

Known Issues

- The following packages are not currently available for Windows:
      affxparser    biomaRt       GeneR         GeneTraffic
      iSPlot        KEGGSOAP      maDB          MANOR
      msbase        pgUtils       RdbiPgSQL     rhdf5
      RMAGEML       SAGElyzer     SBMLR         stam

- The following packages are not currently available for OS X:
      aCGH          edd           RdbiPgSQL     rhdf5
      RMAGEML       xcms

- The genbank() function in package annotate is broken.  The CGI
  script it was accessing at NCBI appears not to be functioning.  You
  will see a message like::

      parser error : Start tag expected, '<' not found
      Content-Type: text/html; charset=UTF-8

- The hexbin package is unable to execute its vignette on Windows.  A
  plot method fails giving an error message about -Inf, Inf xlim. 

- The golubEsets dataset is temporarily unavailable, it will be fixed
  next week.

17 New Packages

Title: Affymetrix File Parsing SDK
Author: James Bullard, Kasper Daniel Hansen

Title: QC Report Generation for affyBatch objects
Author: Craig Parman, Conrad Halling

Title: Compute cluster stability scores for microarray data
Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin

Title: Performs differential gene expression Analysis
Author: Choudary Jagarlamudi

Title: Vector objects for R with external storage
Author: Saikat DebRoy

Title: FDR adjustments of Microarray Experiments (FDR-AME)
Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli

Title: Calculates a global test for differential gene expression
Author: U. Mansmann, R. Meister

Title: Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Author: HyungJun Cho

Title: Significant Gene Expression Profile Differeneces in Time Course Microarray Data
Author: Ana Conesa, Maria José Nueda

Title: Tools for analyzing Micro Array experiments
Author: Hao Wu <hao at jax.org>, with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui

Title: Micro-Array NORmalization
Author: Pierre Neuvial, Philippe Hupé

Title: multi-chip modified gamma Model of Oligonucleotide Signal
Author: Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence

Title: Classification of Microarray Samples using Penalized Discriminant Methods
Author: James W. MacDonald, Debashis Ghosh, based in part on 

Title: Regional Expression Biases
Author: Kyle A. Furge and Karl Dykema

Title: Computationally simulates the AP-MS technology.
Author: Tony Chiang <tchiang at fhcrc.org>

Title: SBML-R Interface and Analysis Tools
Author: Tomas Radivoyevitch

Title: Statistical Analysis for Developmental Microarray Time Course Data
Author: Yu Chuan Tai 

Best Wishes,

+ seth
For the Bioconductor Core Team

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