Welcome to the NuGO R-server!

Message 25 October 2010:

A table listing the Bioconductor 2.7 packages is created (see below).

Message 18 October 2010:

The repository is set on the 2.7 release. To install older releases, please try:
  install.packages(repos="http://nugo-r.bioinformatics.nl/2.x/bioc/") or,
  install.packages(repos="http://nugo-r.bioinformatics.nl/2.x/bioc-previous/")

or browse through the packages listed below.


(Older messages are moved to the bottom of this page).

Older libraries are available here (<= R-2.9.x), here (R-2.10.x), and here (R-2.11.x).


Page contents:

On this page, you can find R/Bioconductor libraries for Unix/Linux and Windows:
1. Bioconductor support libraries for the human and mouse NuGO arrays.
2. Bioconductor annotation libraries for the Affymetrix Gene Titan system.
3. Bioconductor libraries for the MBNI Custom Chip Definition Files (CDFs) for the human and mouse NuGO arrays (cdf, probe, and Entrez gene annotation).
4. For the current MBNI Custom Chip Definition Files (CDFs) release: Bioconductor libraries for human, mouse, and rat species that we support (Entrez gene; also probe and cdf)*.
5. For the previous MBNI Custom Chip Definition Files (CDFs) release: Bioconductor libraries for human, mouse, and rat species that we support (Entrez gene; also probe and cdf)*.

*: For convenience, we mirror the probe and CDF files as provided by MBNI. The annotation libraries are created by ourselves. We provide only the Entrezg libraries, and tairg for Arabidopsis.


REMARK: we decided to use the ENTREZ Custom CDF-files for the following reasons:
Off course, you are free to use one of the other formats, e.g. ENSEMBL, but we do not provide Bioconductor annotation libraries for those custom CDFs.

Fast installation

NuGO arrays (Affymetrix):
    source("http://www.bioconductor.org/biocLite.R")
    biocLite(c("nugohs1a520180hsentrezg.db", "nugohs1a520180hsentrezgcdf", "nugohs1a520180hsentrezgprobe"))
    biocLite(c("nugomm1a520177mmentrezg.db", "nugomm1a520177mmentrezgcdf", "nugomm1a520177mmentrezgprobe"))

hs: human microarrays; mm: mouse microarrays, and YES: these libraries are officially supported via Bioconductor!

Custom CDFs:
Please do this if you receive an error message on missing libraries (only the lacking libraries need to be installed):
    source("http://www.bioconductor.org/biocLite.R")
    biocLite(c("org.At.tair.db", "org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db"))

NuGO arrays (Custom CDF - current):
    install.packages(pkgs = c("nugohs1a520180hsentrezg.db", "nugohs1a520180hsentrezgcdf", "nugohs1a520180hsentrezgprobe"), repos = "http://nugo-r.bioinformatics.nl/bioc")
    install.packages(pkgs = c("nugomm1a520177mmentrezg.db", "nugomm1a520177mmentrezgcdf", "nugomm1a520177mmentrezgprobe"), repos = "http://nugo-r.bioinformatics.nl/bioc")

NuGO arrays (Custom CDF - previous):
    install.packages(pkgs = c("nugohs1a520180hsentrezg.db", "nugohs1a520180hsentrezgcdf", "nugohs1a520180hsentrezgprobe"), repos = "http://nugo-r.bioinformatics.nl/bioc-previous")
    install.packages(pkgs = c("nugomm1a520177mmentrezg.db", "nugomm1a520177mmentrezgcdf", "nugomm1a520177mmentrezgprobe"), repos ="http://nugo-r.bioinformatics.nl/bioc-previous")

Current Custom CDf is version 13.0.0 (28 July 2010). Previous Custom CDF is version 12.0.2 (26 April 2010).
If new Custom CDF libraries are released, the versions will shift up (and the current "previous" repository will be dropped).
Please check the tables below to see whether your chip is supported! Simply use the proper library names in the commands as shown in the examples above.

Manual Installation

Installation instructions

For Windows: download the appropriate .zip-files from the tables below. In RGui, go to Packages => Install package(s) from local zip-files... Browse to the location where you downloaded your .zip-files and select the files you want to install. Done!

For Unix/Linux: download the appropriate .tar.gz files from the tables below. cd to the directory where you downloaded your .tar.gz files and execute the following command (multiple times for multiple .tar.gz files): R CMD INSTALL <your downloaded .tar.gz file>.

Download tables

1. Human and mouse NuGO array support files as provided on the Bioconductor web site (25 October 2010).
    Here, also the CDF and PROBE libraries are available for download. To obtain full microarray support, you need to download and install all three libraries for each chip!
Affymetrix array type Linux/Unix
Windows
Human NuGO Array (nugohs1a520180) nugohs1a520180.db_2.2.0.tar.gz
nugohs1a520180cdf_2.2.0.tar.gz
nugohs1a520180probe_2.2.0.tar.gz
nugohs1a520180.db_2.2.0.zip
nugohs1a520180cdf_2.2.0.zip
nugohs1a520180probe_2.2.0.zip
Mouse NuGO Array (nugomm1a520177) nugomm1a520177.db_2.2.0.tar.gz
nugomm1a520177cdf_2.2.0.tar.gz
nugomm1a520177probe_2.2.0.tar.gz
nugomm1a520177.db_2.2.0.zip
nugomm1a520177cdf_2.2.0.zip
nugomm1a520177probe_2.2.0.zip

2. Human and mouse NuGO array support files (VERSION 13.0.0; MBNI Custom CDF; updated 25 October 2010).
    Here, also the CDF and PROBE libraries are available for download. To obtain full microarray support, you need to download and install all three libraries for each chip!
Affymetrix array type Linux/Unix Windows
Human NuGO array (nugohs1a520180) nugohs1a520180hsentrezg.db_13.0.1.tar.gz
nugohs1a520180hsentrezgcdf_13.0.0.tar.gz
nugohs1a520180hsentrezgprobe_13.0.0.tar.gz
nugohs1a520180hsentrezg.db_13.0.1.zip
nugohs1a520180hsentrezgcdf_13.0.0.zip
nugohs1a520180hsentrezgprobe_13.0.0.zip
Mouse NuGO array (nugomm1a520177) nugomm1a520177mmentrezg.db_13.0.1.tar.gz
nugomm1a520177mmentrezgcdf_13.0.0.tar.gz
nugomm1a520177mmentrezgprobe_13.0.0.tar.gz
nugomm1a520177mmentrezg.db_13.0.1.zip
nugomm1a520177mmentrezgcdf_13.0.0.zip
nugomm1a520177mmentrezgprobe_13.0.0.zip

3. Annotation libraries for the Affymetrix GeneTitan plates (based on the AFFYMATRIX probe annotations). Updated 25 October 2010).
    The CDF and PROBE libraries are available on http://www.bioconductor.org or via the biocLite() command.
    To obtain full microarray support, you need to download and install all three libraries for each chip!
Affymetrix array type Linux/Unix Windows
Affymetrix GeneTitan plate hthgu133pluspm hthgu133pluspm.db_13.0.1.tar.gz hthgu133pluspm.db_13.0.1.zip
Affymetrix GeneTitan plate htmg430a
htmg430a.db_13.0.1.tar.gz htmg430a.db_13.0.1.zip
Affymetrix GeneTitan plate htmg430b htmg430b.db_13.0.1.tar.gz htmg430b.db_13.0.1.zip
Affymetrix GeneTitan plate htmg430pm
htmg430pm.db_13.0.1.tar.gz htmg430pm.db_13.0.1.zip
Affymetrix GeneTitan plate htrat230pm
htrat230pm.db_13.0.1.tar.gz htrat230pm.db_13.0.1.zip
Affymetrix GeneTitan plate htratfocus
htratfocus.db_13.0.1.tar.gz htratfocus.db_13.0.1.zip

4. Annotation libraries for the MBNI Custom CDF annotation files (VERSION 13.0.1; updated 25 October 2010).
    Here, also the CDF and PROBE libraries are available for download. To obtain full microarray support, you need to download and install all three libraries for each chip!
Affymetrix array type
Linux/Unix
Windows
Arabidopsis thaliana (ath1121501attairg)
ath1121501attairg.db_13.0.1.tar.gz
ath1121501attairgcdf_13.0.0.tar.gz
ath1121501attairgprobe_13.0.0.tar.gz
ath1121501attairg.db_13.0.1.zip
ath1121501attairgcdf_13.0.0.zip
ath1121501attairgprobe_13.0.0.zip
Arabidopsis thaliana (tilingatsnptilx520433attairg) tilingatsnptilx520433attairg.db_13.0.1.tar.gz
tilingatsnptilx520433attairgcdf_13.0.0.tar.gz
tilingatsnptilx520433attairgprobe_13.0.0.tar.gz
tilingatsnptilx520433attairg.db_13.0.1.zip
tilingatsnptilx520433attairgcdf_13.0.0.zip
tilingatsnptilx520433attairgprobe_13.0.0.zip

Bos taurus (bovinebtentrezg)

bovinebtentrezg.db_13.0.1.tar.gz
bovinebtentrezgcdf_13.0.0.tar.gz
bovinebtentrezgprobe_13.0.0.tar.gz
bovinebtentrezg.db_13.0.1.zip
bovinebtentrezgcdf_13.0.0.zip
bovinebtentrezgprobe_13.0.0.zip
Homo sapiens hgfocus
hgfocushsentrezg.db_13.0.1.tar.gz
hgfocushsentrezgcdf_13.0.0.tar.gz
hgfocushsentrezgprobe_13.0.0.tar.gz
hgfocushsentrezg.db_13.0.1.zip
hgfocushsentrezgcdf_13.0.0.zip
hgfocushsentrezgprobe_13.0.0.zip
Homo sapiens hgu133a2
hgu133a2hsentrezg.db_13.0.1.tar.gz
hgu133a2hsentrezgcdf_13.0.0.tar.gz
hgu133a2hsentrezgprobe_13.0.0.tar.gz
hgu133a2hsentrezg.db_13.0.1.zip
hgu133a2hsentrezgcdf_13.0.0.zip
hgu133a2hsentrezgprobe_13.0.0.zip
Homo sapiens hgu133a
hgu133ahsentrezg.db_13.0.1.tar.gz
hgu133ahsentrezgcdf_13.0.0.tar.gz
hgu133ahsentrezgprobe_13.0.0.tar.gz
hgu133ahsentrezg.db_13.0.1.zip
hgu133ahsentrezgcdf_13.0.0.zip
hgu133ahsentrezgprobe_13.0.0.zip
Homo sapiens hthgu133a (GeneTitan plates)
hthgu133ahsentrezg.db_13.0.1.tar.gz
hthgu133ahsentrezgcdf_13.0.0.tar.gz
hthgu133ahsentrezgprobe_13.0.0.tar.gz
hthgu133ahsentrezg.db_13.0.1.zip
hthgu133ahsentrezgcdf_13.0.0.zip
hthgu133ahsentrezgprobe_13.0.0.zip
Homo Sapiens hgu133b
hgu133bhsentrezg.db_13.0.1.tar.gz
hgu133bhsentrezgcdf_13.0.0.tar.gz
hgu133bhsentrezgprobe_13.0.0.tar.gz
hgu133bhsentrezg.db_13.0.1.zip
hgu133bhsentrezgcdf_13.0.0.zip
hgu133bhsentrezgprobe_13.0.0.zip
Homo sapiens hthgu133b (GeneTitan plates) hthgu133bhsentrezg.db_13.0.1.tar.gz
hthgu133bhsentrezgcdf_13.0.0.tar.gz
hthgu133bhsentrezgprobe_13.0.0.tar.gz
hthgu133bhsentrezg.db_13.0.1.zip
hthgu133bhsentrezgcdf_13.0.0.zip
hthgu133bhsentrezgprobe_13.0.0.zip
Homo Sapiens hgu133plus2
hgu133plus2hsentrezg.db_13.0.1.tar.gz
hgu133plus2hsentrezgcdf_13.0.0.tar.gz
hgu133plus2hsentrezgprobe_13.0.0.tar.gz
hgu133plus2hsentrezg.db_13.0.1.zip
hgu133plus2hsentrezgcdf_13.0.0.zip
hgu133plus2hsentrezgprobe_13.0.0.zip
Homo sapiens hthgu133pluspm (GeneTitan plates) hthgu133pluspmhsentrezg.db_13.0.1.tar.gz
hthgu133pluspmhsentrezgcdf_13.0.0.tar.gz
hthgu133pluspmhsentrezgprobe_13.0.0.tar.gz
hthgu133pluspmhsentrezg.db_13.0.1.zip
hthgu133pluspmhsentrezgcdf_13.0.0.zip
hthgu133pluspmhsentrezgprobe_13.0.0.zip
Homo Sapiens hgu95av2
hgu95av2hsentrezg.db_13.0.1.tar.gz
hgu95av2hsentrezgcdf_13.0.0.tar.gz
hgu95av2hsentrezgprobe_13.0.0.tar.gz
hgu95av2hsentrezg.db_13.0.1.zip
hgu95av2hsentrezgcdf_13.0.0.zip
hgu95av2hsentrezgprobe_13.0.0.zip

Homo Sapiens hgu95a

hgu95ahsentrezg.db_13.0.1.tar.gz
hgu95ahsentrezgcdf_13.0.0.tar.gz
hgu95ahsentrezgprobe_13.0.0.tar.gz
hgu95ahsentrezg.db_13.0.1.zip
hgu95ahsentrezgcdf_13.0.0.zip
hgu95ahsentrezgprobe_13.0.0.zip
Homo Sapiens hgu95b
hgu95bhsentrezg.db_13.0.1.tar.gz
hgu95bhsentrezgcdf_13.0.0.tar.gz
hgu95bhsentrezgprobe_13.0.0.tar.gz
hgu95bhsentrezg.db_13.0.1.zip
hgu95bhsentrezgcdf_13.0.0.zip
hgu95bhsentrezgprobe_13.0.0.zip
Homo Sapiens hgu95c
hgu95chsentrezg.db_13.0.1.tar.gz
hgu95chsentrezgcdf_13.0.0.tar.gz
hgu95chsentrezgprobe_13.0.0.tar.gz
hgu95chsentrezg.db_13.0.1.zip
hgu95chsentrezgcdf_13.0.0.zip
hgu95chsentrezgprobe_13.0.0.zip
Homo Sapiens hgu95d
hgu95dhsentrezg.db_13.0.1.tar.gz
hgu95dhsentrezgcdf_13.0.0.tar.gz
hgu95dhsentrezgprobe_13.0.0.tar.gz
hgu95dhsentrezg.db_13.0.1.zip
hgu95dhsentrezgcdf_13.0.0.zip
hgu95dhsentrezgprobe_13.0.0.zip
Homo Sapiens hgu95e
hgu95ehsentrezg.db_13.0.1.tar.gz
hgu95ehsentrezgcdf_13.0.0.tar.gz
hgu95ehsentrezgprobe_13.0.0.tar.gz
hgu95ehsentrezg.db_13.0.1.zip
hgu95ehsentrezgcdf_13.0.0.zip
hgu95ehsentrezgprobe_13.0.0.zip

Homo sapiens hcg110

hcg110hsentrezg.db_13.0.1.tar.gz
hcg110hsentrezgcdf_13.0.0.tar.gz
hcg110hsentrezgprobe_13.0.0.tar.gz
hcg110hsentrezg.db_13.0.1.zip
hcg110hsentrezgcdf_13.0.0.zip
hcg110hsentrezgprobe_13.0.0.zip

Homo sapiens hgu219

hgu219hsentrezg.db_13.0.1.tar.gz
hgu219hsentrezgcdf_13.0.0.tar.gz
hgu219hsentrezgprobe_13.0.0.tar.gz
hgu219hsentrezg.db_13.0.1.zip
hgu219hsentrezgcdf_13.0.0.zip
hgu219hsentrezgprobe_13.0.0.zip

Homo sapiens hu6800

hu6800hsentrezg.db_13.0.1.tar.gz
hu6800hsentrezgcdf_13.0.0.tar.gz
hu6800hsentrezgprobe_13.0.0.tar.gz
hu6800hsentrezg.db_13.0.1.zip
hu6800hsentrezgcdf_13.0.0.zip
hu6800hsentrezgprobe_13.0.0.zip
Homo sapiens 133x3p
u133x3phsentrezg.db_13.0.1.tar.gz
u133x3phsentrezgcdf_13.0.0.tar.gz
u133x3phsentrezgprobe_13.0.0.tar.gz
u133x3phsentrezg.db_13.0.1.zip
u133x3phsentrezgcdf_13.0.0.zip
u133x3phsentrezgprobe_13.0.0.zip
Homo sapiens hugene10stv1
hugene10stv1hsentrezg.db_13.0.1.tar.gz
hugene10stv1hsentrezgcdf_13.0.0.tar.gz
hugene10stv1hsentrezgprobe_13.0.0.tar.gz
hugene10stv1hsentrezg.db_13.0.1.zip
hugene10stv1hsentrezgcdf_13.0.0.zip
hugene10stv1hsentrezgprobe_13.0.0.zip

Homo sapiens hugene11stv1

hugene11stv1hsentrezg.db_13.0.1.tar.gz
hugene11stv1hsentrezgcdf_13.0.0.tar.gz
hugene11stv1hsentrezgprobe_13.0.0.tar.gz
hugene11stv1hsentrezg.db_13.0.1.zip
hugene11stv1hsentrezgcdf_13.0.0.zip
hugene11stv1hsentrezgprobe_13.0.0.zip
Mus musculus mgu74av2
mgu74av2mmentrezg.db_13.0.1.tar.gz
mgu74av2mmentrezgcdf_13.0.0.tar.gz
mgu74av2mmentrezgprobe_13.0.0.tar.gz
mgu74av2mmentrezg.db_13.0.1.zip
mgu74av2mmentrezgcdf_13.0.0.zip
mgu74av2mmentrezgprobe_13.0.0.zip
Mus musculus mgu74bv2
mgu74bv2mmentrezg.db_13.0.1.tar.gz
mgu74bv2mmentrezgcdf_13.0.0.tar.gz
mgu74bv2mmentrezgprobe_13.0.0.tar.gz
mgu74bv2mmentrezg.db_13.0.1.zip
mgu74bv2mmentrezgcdf_13.0.0.zip
mgu74bv2mmentrezgprobe_13.0.0.zip
Mus musculus mgu74cv2
mgu74cv2mmentrezg.db_13.0.1.tar.gz
mgu74cv2mmentrezgcdf_13.0.0.tar.gz
mgu74cv2mmentrezgprobe_13.0.0.tar.gz
mgu74cv2mmentrezg.db_13.0.1.zip
mgu74cv2mmentrezgcdf_13.0.0.zip
mgu74cv2mmentrezgprobe_13.0.0.zip
Mus musculus moe430a
moe430ammentrezg.db_13.0.1.tar.gz
moe430ammentrezgcdf_13.0.0.tar.gz
moe430ammentrezgprobe_13.0.0.tar.gz
moe430ammentrezg.db_13.0.1.zip
moe430ammentrezgcdf_13.0.0.zip
moe430ammentrezgprobe_13.0.0.zip
Mus musculus htmg430a (GeneTitan plates)
htmg430ammentrezg.db_13.0.1.tar.gz
htmg430ammentrezgcdf_13.0.0.tar.gz
htmg430ammentrezgprobe_13.0.0.tar.gz
htmg430ammentrezg.db_13.0.1.zip
htmg430ammentrezgcdf_13.0.0.zip
htmg430ammentrezgprobe_13.0.0.zip
Mus musculus moe430b
moe430bmmentrezg.db_13.0.1.tar.gz
moe430bmmentrezgcdf_13.0.0.tar.gz
moe430bmmentrezgprobe_13.0.0.tar.gz
moe430bmmentrezg.db_13.0.1.zip
moe430bmmentrezgcdf_13.0.0.zip
moe430bmmentrezgprobe_13.0.0.zip
Mus musculus htmg430b (GeneTitan plates) htmg430bmmentrezg.db_13.0.1.tar.gz
htmg430bmmentrezgcdf_13.0.0.tar.gz
htmg430bmmentrezgprobe_13.0.0.tar.gz
htmg430bmmentrezg.db_13.0.1.zip
htmg430bmmentrezgcdf_13.0.0.zip
htmg430bmmentrezgprobe_13.0.0.zip
Mus musculus moe430a2
mouse430a2mmentrezg.db_13.0.1.tar.gz
mouse430a2mmentrezgcdf_13.0.0.tar.gz
mouse430a2mmentrezgprobe_13.0.0.tar.gz
mouse430a2mmentrezg.db_13.0.1.zip
mouse430a2mmentrezgcdf_13.0.0.zip
mouse430a2mmentrezgprobe_13.0.0.zip
Mus musculus mouse4302
mouse4302mmentrezg.db_13.0.1.tar.gz
mouse4302mmentrezgcdf_13.0.0.tar.gz
mouse4302mmentrezgprobe_13.0.0.tar.gz
mouse4302mmentrezg.db_13.0.1.zip
mouse4302mmentrezgcdf_13.0.0.zip
mouse4302mmentrezgprobe_13.0.0.zip
Mus musculus htmg430pm (GeneTitan plates)
htmg430pmmmentrezg.db_13.0.1.tar.gz
htmg430pmmmentrezgcdf_13.0.0.tar.gz
htmg430pmmmentrezgprobe_13.0.0.tar.gz
htmg430pmmmentrezg.db_13.0.1.zip
htmg430pmmmentrezgcdf_13.0.0.zip
htmg430pmmmentrezgprobe_13.0.0.zip
Mus musculus mogene10stv1
mogene10stv1mmentrezg.db_13.0.1.tar.gz
mogene10stv1mmentrezgcdf_13.0.0.tar.gz
mogene10stv1mmentrezgprobe_13.0.0.tar.gz
mogene10stv1mmentrezg.db_13.0.1.zip
mogene10stv1mmentrezgcdf_13.0.0.zip
mogene10stv1mmentrezgprobe_13.0.0.zip

Mus musculus mogene11stv1

mogene11stv1mmentrezg.db_13.0.1.tar.gz
mogene11stv1mmentrezgcdf_13.0.0.tar.gz
mogene11stv1mmentrezgprobe_13.0.0.tar.gz
mogene11stv1mmentrezg.db_13.0.1.zip
mogene11stv1mmentrezgcdf_13.0.0.zip
mogene11stv1mmentrezgprobe_13.0.0.zip

Sus scrofa porcine

porcinessentrezg.db_13.0.1.tar.gz
porcinessentrezgcdf_13.0.0.tar.gz
porcinessentrezgprobe_13.0.0.tar.gz
porcinessentrezg.db_13.0.1.zip
porcinessentrezgcdf_13.0.0.zip
porcinessentrezgprobe_13.0.0.zip
Rattus norvegicus rae230a
rae230arnentrezg.db_13.0.1.tar.gz
rae230arnentrezgcdf_13.0.0.tar.gz
rae230arnentrezgprobe_13.0.0.tar.gz
rae230arnentrezg.db_13.0.1.zip
rae230arnentrezgcdf_13.0.0.zip
rae230arnentrezgprobe_13.0.0.zip
Rattus norvegicus rae230b
rae230brnentrezg.db_13.0.1.tar.gz
rae230brnentrezgcdf_13.0.0.tar.gz
rae230brnentrezgprobe_13.0.0.tar.gz
rae230brnentrezg.db_13.0.1.zip
rae230brnentrezgcdf_13.0.0.zip
rae230brnentrezgprobe_13.0.0.zip
Rattus norvegicus rat2302
rat2302rnentrezg.db_13.0.1.tar.gz
rat2302rnentrezgcdf_13.0.0.tar.gz
rat2302rnentrezgprobe_13.0.0.tar.gz
rat2302rnentrezg.db_13.0.1.zip
rat2302rnentrezgcdf_13.0.0.zip
rat2302rnentrezgprobe_13.0.0.zip
Rattus norvegicus htrat230pm (GeneTitan plates)
htrat230pmrnentrezg.db_13.0.1.tar.gz
htrat230pmrnentrezgcdf_13.0.0.tar.gz
htrat230pmrnentrezgprobe_13.0.0.tar.gz
htrat230pmrnentrezg.db_13.0.1.zip
htrat230pmrnentrezgcdf_13.0.0.zip
htrat230pmrnentrezgprobe_13.0.0.zip
Rattus norvegicus rgu34a
rgu34arnentrezg.db_13.0.1.tar.gz
rgu34arnentrezgcdf_13.0.0.tar.gz
rgu34arnentrezgprobe_13.0.0.tar.gz
rgu34arnentrezg.db_13.0.1.zip
rgu34arnentrezgcdf_13.0.0.zip
rgu34arnentrezgprobe_13.0.0.zip
Rattus norvegicus rgu34b
rgu34brnentrezg.db_13.0.1.tar.gz
rgu34brnentrezgcdf_13.0.0.tar.gz
rgu34brnentrezgprobe_13.0.0.tar.gz
rgu34brnentrezg.db_13.0.1.zip
rgu34brnentrezgcdf_13.0.0.zip
rgu34brnentrezgprobe_13.0.0.zip
Rattus norvegicus rgu34c
rgu34crnentrezg.db_13.0.1.tar.gz
rgu34crnentrezgcdf_13.0.0.tar.gz
rgu34crnentrezgprobe_13.0.0.tar.gz
rgu34crnentrezg.db_13.0.1.zip
rgu34crnentrezgcdf_13.0.0.zip
rgu34crnentrezgprobe_13.0.0.zip
Rattus norvegicus ragene10stv1
ragene10stv1rnentrezg.db_13.0.1.tar.gz
ragene10stv1rnentrezgcdf_13.0.0.tar.gz
ragene10stv1rnentrezgprobe_13.0.0.tar.gz
ragene10stv1rnentrezg.db_13.0.1.zip
ragene10stv1rnentrezgcdf_13.0.0.zip
ragene10stv1rnentrezgprobe_13.0.0.zip

Rattus norvegicus ragene11stv1

ragene11stv1rnentrezg.db_13.0.1.tar.gz
ragene11stv1rnentrezgcdf_13.0.0.tar.gz
ragene11stv1rnentrezgprobe_13.0.0.tar.gz
ragene11stv1rnentrezg.db_13.0.1.zip
ragene11stv1rnentrezgcdf_13.0.0.zip
ragene11stv1rnentrezgprobe_13.0.0.zip
Rattus norvegicus htratfocus (GeneTitan plates)
htratfocusrnentrezg.db_13.0.1.tar.gz
htratfocusrnentrezgcdf_13.0.0.tar.gz
htratfocusrnentrezgprobe_13.0.0.tar.gz
htratfocusrnentrezg.db_13.0.1.zip
htratfocusrnentrezgcdf_13.0.0.zip
htratfocusrnentrezgprobe_13.0.0.zip

Rattus norvegicus rattoxfx

rattoxfxrnentrezg.db_13.0.1.tar.gz
rattoxfxrnentrezgcdf_13.0.0.tar.gz
rattoxfxrnentrezgprobe_13.0.0.tar.gz
rattoxfxrnentrezg.db_13.0.1.zip
rattoxfxrnentrezgcdf_13.0.0.zip
rattoxfxrnentrezgprobe_13.0.0.zip

Rattus norvegicus rnu34

rnu34rnentrezg.db_13.0.1.tar.gz
rnu34rnentrezgcdf_13.0.0.tar.gz
rnu34rnentrezgprobe_13.0.0.tar.gz
rnu34rnentrezg.db_13.0.1.zip
rnu34rnentrezgcdf_13.0.0.zip
rnu34rnentrezgprobe_13.0.0.zip

Rattus norvegicus rtu34

rtu34rnentrezg.db_13.0.1.tar.gz
rtu34rnentrezgcdf_13.0.0.tar.gz
rtu34rnentrezgprobe_13.0.0.tar.gz
rtu34rnentrezg.db_13.0.1.zip
rtu34rnentrezgcdf_13.0.0.zip
rtu34rnentrezgprobe_13.0.0.zip

5. Human and mouse NuGO array support files (VERSION 12.0.0; MBNI Custom CDF; 25 October 2010).
    Here, also the CDF and PROBE libraries are available for download. To obtain full microarray support, you need to download and install all three libraries for each chip!
Affymetrix array type Linux/Unix Windows
Human NuGO array (nugohs1a520180) nugohs1a520180hsentrezg.db_12.0.3.tar.gz
nugohs1a520180hsentrezgcdf_12.0.0.tar.gz
nugohs1a520180hsentrezgprobe_12.0.0.tar.gz
nugohs1a520180hsentrezg.db_12.0.3.zip
nugohs1a520180hsentrezgcdf_12.0.0.zip
nugohs1a520180hsentrezgprobe_12.0.0.zip
Mouse NuGO array (nugomm1a520177) nugomm1a520177mmentrezg.db_12.0.3.tar.gz
nugomm1a520177mmentrezgcdf_12.0.0.tar.gz
nugomm1a520177mmentrezgprobe_12.0.0.tar.gz
nugomm1a520177mmentrezg.db_12.0.3.zip
nugomm1a520177mmentrezgcdf_12.0.0.zip
nugomm1a520177mmentrezgprobe_12.0.0.zip

6. Annotation libraries for the MBNI Custom CDF annotation files (VERSION 12.0.0; updated 25 October 2010).
    Here, also the CDF and PROBE libraries are available for download. To obtain full microarray support, you need to download and install all three libraries for each chip!
Affymetrix array type
Linux/Unix
Windows
Arabidopsis thaliana (ath1121501attairg)
ath1121501attairg.db_12.0.3.tar.gz
ath1121501attairgcdf_12.0.0.tar.gz
ath1121501attairgprobe_12.0.0.tar.gz
ath1121501attairg.db_12.0.3.zip
ath1121501attairgcdf_12.0.0.zip
ath1121501attairgprobe_12.0.0.zip
Arabidopsis thaliana (tilingatsnptilx520433attairg) tilingatsnptilx520433attairg.db_12.0.3.tar.gz
tilingatsnptilx520433attairgcdf_12.0.0.tar.gz
tilingatsnptilx520433attairgprobe_12.0.0.tar.gz
tilingatsnptilx520433attairg.db_12.0.3.zip
tilingatsnptilx520433attairgcdf_12.0.0.zip
tilingatsnptilx520433attairgprobe_12.0.0.zip
Homo sapiens hgfocus
hgfocushsentrezg.db_12.0.3.tar.gz
hgfocushsentrezgcdf_12.0.0.tar.gz
hgfocushsentrezgprobe_12.0.0.tar.gz
hgfocushsentrezg.db_12.0.3.zip
hgfocushsentrezgcdf_12.0.0.zip
hgfocushsentrezgprobe_12.0.0.zip
Homo sapiens hgu133a2
hgu133a2hsentrezg.db_12.0.3.tar.gz
hgu133a2hsentrezgcdf_12.0.0.tar.gz
hgu133a2hsentrezgprobe_12.0.0.tar.gz
hgu133a2hsentrezg.db_12.0.3.zip
hgu133a2hsentrezgcdf_12.0.0.zip
hgu133a2hsentrezgprobe_12.0.0.zip
Homo sapiens hgu133a
hgu133ahsentrezg.db_12.0.3.tar.gz
hgu133ahsentrezgcdf_12.0.0.tar.gz
hgu133ahsentrezgprobe_12.0.0.tar.gz
hgu133ahsentrezg.db_12.0.3.zip
hgu133ahsentrezgcdf_12.0.0.zip
hgu133ahsentrezgprobe_12.0.0.zip
Homo sapiens hthgu133a (GeneTitan plates)
hthgu133ahsentrezg.db_12.0.3.tar.gz
hthgu133ahsentrezgcdf_12.0.0.tar.gz
hthgu133ahsentrezgprobe_12.0.0.tar.gz
hthgu133ahsentrezg.db_12.0.3.zip
hthgu133ahsentrezgcdf_12.0.0.zip
hthgu133ahsentrezgprobe_12.0.0.zip
Homo Sapiens hgu133b
hgu133bhsentrezg.db_12.0.3.tar.gz
hgu133bhsentrezgcdf_12.0.0.tar.gz
hgu133bhsentrezgprobe_12.0.0.tar.gz
hgu133bhsentrezg.db_12.0.3.zip
hgu133bhsentrezgcdf_12.0.0.zip
hgu133bhsentrezgprobe_12.0.0.zip
Homo sapiens hthgu133b (GeneTitan plates) hthgu133bhsentrezg.db_12.0.3.tar.gz
hthgu133bhsentrezgcdf_12.0.0.tar.gz
hthgu133bhsentrezgprobe_12.0.0.tar.gz
hthgu133bhsentrezg.db_12.0.3.zip
hthgu133bhsentrezgcdf_12.0.0.zip
hthgu133bhsentrezgprobe_12.0.0.zip
Homo Sapiens hgu133plus2
hgu133plus2hsentrezg.db_12.0.3.tar.gz
hgu133plus2hsentrezgcdf_12.0.0.tar.gz
hgu133plus2hsentrezgprobe_12.0.0.tar.gz
hgu133plus2hsentrezg.db_12.0.3.zip
hgu133plus2hsentrezgcdf_12.0.0.zip
hgu133plus2hsentrezgprobe_12.0.0.zip
Homo sapiens hthgu133pluspm (GeneTitan plates) hthgu133pluspmhsentrezg.db_12.0.3.tar.gz
hthgu133pluspmhsentrezgcdf_12.0.0.tar.gz
hthgu133pluspmhsentrezgprobe_12.0.0.tar.gz
hthgu133pluspmhsentrezg.db_12.0.3.zip
hthgu133pluspmhsentrezgcdf_12.0.0.zip
hthgu133pluspmhsentrezgprobe_12.0.0.zip
Homo Sapiens hgu95av2
hgu95av2hsentrezg.db_12.0.3.tar.gz
hgu95av2hsentrezgcdf_12.0.0.tar.gz
hgu95av2hsentrezgprobe_12.0.0.tar.gz
hgu95av2hsentrezg.db_12.0.3.zip
hgu95av2hsentrezgcdf_12.0.0.zip
hgu95av2hsentrezgprobe_12.0.0.zip
Homo Sapiens hgu95b
hgu95bhsentrezg.db_12.0.3.tar.gz
hgu95bhsentrezgcdf_12.0.0.tar.gz
hgu95bhsentrezgprobe_12.0.0.tar.gz
hgu95bhsentrezg.db_12.0.3.zip
hgu95bhsentrezgcdf_12.0.0.zip
hgu95bhsentrezgprobe_12.0.0.zip
Homo Sapiens hgu95c
hgu95chsentrezg.db_12.0.3.tar.gz
hgu95chsentrezgcdf_12.0.0.tar.gz
hgu95chsentrezgprobe_12.0.0.tar.gz
hgu95chsentrezg.db_12.0.3.zip
hgu95chsentrezgcdf_12.0.0.zip
hgu95chsentrezgprobe_12.0.0.zip
Homo Sapiens hgu95d
hgu95dhsentrezg.db_12.0.3.tar.gz
hgu95dhsentrezgcdf_12.0.0.tar.gz
hgu95dhsentrezgprobe_12.0.0.tar.gz
hgu95dhsentrezg.db_12.0.3.zip
hgu95dhsentrezgcdf_12.0.0.zip
hgu95dhsentrezgprobe_12.0.0.zip
Homo Sapiens hgu95e
hgu95ehsentrezg.db_12.0.3.tar.gz
hgu95ehsentrezgcdf_12.0.0.tar.gz
hgu95ehsentrezgprobe_12.0.0.tar.gz
hgu95ehsentrezg.db_12.0.3.zip
hgu95ehsentrezgcdf_12.0.0.zip
hgu95ehsentrezgprobe_12.0.0.zip
Homo sapiens 133x3p
u133x3phsentrezg.db_12.0.3.tar.gz
u133x3phsentrezgcdf_12.0.0.tar.gz
u133x3phsentrezgprobe_12.0.0.tar.gz
u133x3phsentrezg.db_12.0.3.zip
u133x3phsentrezgcdf_12.0.0.zip
u133x3phsentrezgprobe_12.0.0.zip
Homo sapiens hugene10stv1
hugene10stv1hsentrezg.db_12.0.3.tar.gz
hugene10stv1hsentrezgcdf_12.0.0.tar.gz
hugene10stv1hsentrezgprobe_12.0.0.tar.gz
hugene10stv1hsentrezg.db_12.0.3.zip
hugene10stv1hsentrezgcdf_12.0.0.zip
hugene10stv1hsentrezgprobe_12.0.0.zip
Homo sapiens huex10stv2
huex10stv2hsentrezg.db_12.0.3.tar.gz
huex10stv2hsentrezgcdf_12.0.0.tar.gz
huex10stv2hsentrezgprobe_12.0.0.tar.gz
huex10stv2hsentrezg.db_12.0.3.zip
huex10stv2hsentrezgcdf_12.0.0.zip
huex10stv2hsentrezgprobe_12.0.0.zip
Mus musculus mgu74av2
mgu74av2mmentrezg.db_12.0.3.tar.gz
mgu74av2mmentrezgcdf_12.0.0.tar.gz
mgu74av2mmentrezgprobe_12.0.0.tar.gz
mgu74av2mmentrezg.db_12.0.3.zip
mgu74av2mmentrezgcdf_12.0.0.zip
mgu74av2mmentrezgprobe_12.0.0.zip
Mus musculus mgu74bv2
mgu74bv2mmentrezg.db_12.0.3.tar.gz
mgu74bv2mmentrezgcdf_12.0.0.tar.gz
mgu74bv2mmentrezgprobe_12.0.0.tar.gz
mgu74bv2mmentrezg.db_12.0.3.zip
mgu74bv2mmentrezgcdf_12.0.0.zip
mgu74bv2mmentrezgprobe_12.0.0.zip
Mus musculus mgu74cv2
mgu74cv2mmentrezg.db_12.0.3.tar.gz
mgu74cv2mmentrezgcdf_12.0.0.tar.gz
mgu74cv2mmentrezgprobe_12.0.0.tar.gz
mgu74cv2mmentrezg.db_12.0.3.zip
mgu74cv2mmentrezgcdf_12.0.0.zip
mgu74cv2mmentrezgprobe_12.0.0.zip
Mus musculus moe430a
moe430ammentrezg.db_12.0.3.tar.gz
moe430ammentrezgcdf_12.0.0.tar.gz
moe430ammentrezgprobe_12.0.0.tar.gz
moe430ammentrezg.db_12.0.3.zip
moe430ammentrezgcdf_12.0.0.zip
moe430ammentrezgprobe_12.0.0.zip
Mus musculus htmg430a (GeneTitan plates)
htmg430ammentrezg.db_12.0.3.tar.gz
htmg430ammentrezgcdf_12.0.0.tar.gz
htmg430ammentrezgprobe_12.0.0.tar.gz
htmg430ammentrezg.db_12.0.3.zip
htmg430ammentrezgcdf_12.0.0.zip
htmg430ammentrezgprobe_12.0.0.zip
Mus musculus moe430b
moe430bmmentrezg.db_12.0.3.tar.gz
moe430bmmentrezgcdf_12.0.0.tar.gz
moe430bmmentrezgprobe_12.0.0.tar.gz
moe430bmmentrezg.db_12.0.3.zip
moe430bmmentrezgcdf_12.0.0.zip
moe430bmmentrezgprobe_12.0.0.zip
Mus musculus htmg430b (GeneTitan plates) htmg430bmmentrezg.db_12.0.3.tar.gz
htmg430bmmentrezgcdf_12.0.0.tar.gz
htmg430bmmentrezgprobe_12.0.0.tar.gz
htmg430bmmentrezg.db_12.0.3.zip
htmg430bmmentrezgcdf_12.0.0.zip
htmg430bmmentrezgprobe_12.0.0.zip
Mus musculus moe430a2
mouse430a2mmentrezg.db_12.0.3.tar.gz
mouse430a2mmentrezgcdf_12.0.0.tar.gz
mouse430a2mmentrezgprobe_12.0.0.tar.gz
mouse430a2mmentrezg.db_12.0.3.zip
mouse430a2mmentrezgcdf_12.0.0.zip
mouse430a2mmentrezgprobe_12.0.0.zip
Mus musculus mouse4302
mouse4302mmentrezg.db_12.0.3.tar.gz
mouse4302mmentrezgcdf_12.0.0.tar.gz
mouse4302mmentrezgprobe_12.0.0.tar.gz
mouse4302mmentrezg.db_12.0.3.zip
mouse4302mmentrezgcdf_12.0.0.zip
mouse4302mmentrezgprobe_12.0.0.zip
Mus musculus htmg430pm (GeneTitan plates)
htmg430pmmmentrezg.db_12.0.3.tar.gz
htmg430pmmmentrezgcdf_12.0.0.tar.gz
htmg430pmmmentrezgprobe_12.0.0.tar.gz
htmg430pmmmentrezg.db_12.0.3.zip
htmg430pmmmentrezgcdf_12.0.0.zip
htmg430pmmmentrezgprobe_12.0.0.zip
Mus musculus mogene10stv1
mogene10stv1mmentrezg.db_12.0.3.tar.gz
mogene10stv1mmentrezgcdf_12.0.0.tar.gz
mogene10stv1mmentrezgprobe_12.0.0.tar.gz
mogene10stv1mmentrezg.db_12.0.3.zip
mogene10stv1mmentrezgcdf_12.0.0.zip
mogene10stv1mmentrezgprobe_12.0.0.zip
Mus musculus moex10stv1
moex10stv1mmentrezg.db_12.0.3.tar.gz
moex10stv1mmentrezgcdf_12.0.0.tar.gz
moex10stv1mmentrezgprobe_12.0.0.tar.gz
moex10stv1mmentrezg.db_12.0.3.zip
moex10stv1mmentrezgcdf_12.0.0.zip
moex10stv1mmentrezgprobe_12.0.0.zip
Rattus norvegicus rae230a
rae230arnentrezg.db_12.0.3.tar.gz
rae230arnentrezgcdf_12.0.0.tar.gz
rae230arnentrezgprobe_12.0.0.tar.gz
rae230arnentrezg.db_12.0.3.zip
rae230arnentrezgcdf_12.0.0.zip
rae230arnentrezgprobe_12.0.0.zip
Rattus norvegicus rae230b
rae230brnentrezg.db_12.0.3.tar.gz
rae230brnentrezgcdf_12.0.0.tar.gz
rae230brnentrezgprobe_12.0.0.tar.gz
rae230brnentrezg.db_12.0.3.zip
rae230brnentrezgcdf_12.0.0.zip
rae230brnentrezgprobe_12.0.0.zip
Rattus norvegicus rat2302
rat2302rnentrezg.db_12.0.3.tar.gz
rat2302rnentrezgcdf_12.0.0.tar.gz
rat2302rnentrezgprobe_12.0.0.tar.gz
rat2302rnentrezg.db_12.0.3.zip
rat2302rnentrezgcdf_12.0.0.zip
rat2302rnentrezgprobe_12.0.0.zip
Rattus norvegicus htrat230pm (GeneTitan plates)
htrat230pmrnentrezg.db_12.0.3.tar.gz
htrat230pmrnentrezgcdf_12.0.0.tar.gz
htrat230pmrnentrezgprobe_12.0.0.tar.gz
htrat230pmrnentrezg.db_12.0.3.zip
htrat230pmrnentrezgcdf_12.0.0.zip
htrat230pmrnentrezgprobe_12.0.0.zip
Rattus norvegicus rgu34a
rgu34arnentrezg.db_12.0.3.tar.gz
rgu34arnentrezgcdf_12.0.0.tar.gz
rgu34arnentrezgprobe_12.0.0.tar.gz
rgu34arnentrezg.db_12.0.3.zip
rgu34arnentrezgcdf_12.0.0.zip
rgu34arnentrezgprobe_12.0.0.zip
Rattus norvegicus rgu34b
rgu34brnentrezg.db_12.0.3.tar.gz
rgu34brnentrezgcdf_12.0.0.tar.gz
rgu34brnentrezgprobe_12.0.0.tar.gz
rgu34brnentrezg.db_12.0.3.zip
rgu34brnentrezgcdf_12.0.0.zip
rgu34brnentrezgprobe_12.0.0.zip
Rattus norvegicus rgu34c
rgu34crnentrezg.db_12.0.3.tar.gz
rgu34crnentrezgcdf_12.0.0.tar.gz
rgu34crnentrezgprobe_12.0.0.tar.gz
rgu34crnentrezg.db_12.0.3.zip
rgu34crnentrezgcdf_12.0.0.zip
rgu34crnentrezgprobe_12.0.0.zip
Rattus norvegicus ragene10stv1
ragene10stv1rnentrezg.db_12.0.3.tar.gz
ragene10stv1rnentrezgcdf_12.0.0.tar.gz
ragene10stv1rnentrezgprobe_12.0.0.tar.gz
ragene10stv1rnentrezg.db_12.0.3.zip
ragene10stv1rnentrezgcdf_12.0.0.zip
ragene10stv1rnentrezgprobe_12.0.0.zip
Rattus norvegicus raex10stv1
raex10stv1rnentrezg.db_12.0.3.tar.gz
raex10stv1rnentrezgcdf_12.0.0.tar.gz
raex10stv1rnentrezgprobe_12.0.0.tar.gz
raex10stv1rnentrezg.db_12.0.3.zip
raex10stv1rnentrezgcdf_12.0.0.zip
raex10stv1rnentrezgprobe_12.0.0.zip
Rattus norvegicus htratfocus (GeneTitan plates)
htratfocusrnentrezg.db_12.0.3.tar.gz
htratfocusrnentrezgcdf_12.0.0.tar.gz
htratfocusrnentrezgprobe_12.0.0.tar.gz
htratfocusrnentrezg.db_12.0.3.zip
htratfocusrnentrezgcdf_12.0.0.zip
htratfocusrnentrezgprobe_12.0.0.zip


Old Messages

Message 30 September 2010:

1.  MBNI Custom CDF libraries (version 13.0.0), including the annotation libraries feasible for R-2.12.x (version 13.0.1), are available via:

          install.packages(repos="http://nugo-r.bioinformatics.nl/2.7/bioc/")

     Please select the packages that you need from the list of available packages.


2.  MBNI Custom CDF libraries (version 12.0.0), including the annotation libraries feasible for R-2.12.x (version 12.0.3), are available via:

          install.packages(repos="http://nugo-r.bioinformatics.nl/2.7/bioc-previous/")

     Please select the packages that you need from the list of available packages.
     NOTE!! You need to install the library matchprobes (included in this repository) to properly use the MBNI version 12.0.0 / 12.0.3 libraries!

3.  Affymetrix GeneTitan annotation libraries, which are not supported by Bioconductor, can be installed as follows:

          install.packages(pkgs = c("htratfocus.db", "htrat230pm.db", "htmg430pm.db", "htmg430b.db", "htmg430a.db", "hthgu133pluspm.db"),
          repos ="http://nugo-r.bioinformatics.nl/2.7/bioc")


     NOTE: The library
"hgu219.db" is available via the Bioconductor repository starting from version 2.7.


The new Bioconductor release (version 2.7) is scheduled for October 18. After the release, these packages will become the default installation packages.

Contact:

Dr. Philip de Groot PhD
Nutrition, Metabolism and Genomics group
Division of Human Nutrition
Wageningen University
PO Box 8129
6700 EV Wageningen
The Netherlands
Phone: +31-317-485786
Fax:     +31-317-483342
Philip.deGroot@wur.nl

Additional information:
Nutrigenomics Consortium
TI Food & Nutrition
Wageningen University



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(This page is last modified on 26 August 2010).