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Index:

  1. annmap Human Database
  2. annmap Mouse Database
  3. annmap Rat Database
  4. annmap Pombe Database
  5. annmap Cerevisiae Database
  6. Stored Procedure patch for xmapcore v1.2.5+
  7. AnnmapBridge
  8. Human Exon CDF
  9. Mouse Exon CDF
  10. Rat Exon CDF
  11. Old "exonmap" Human Database
  12. Old "exonmap" Mouse Database
  13. Old "exonmap" Rat Database

annmap Human Database

Annmap is the replacement for the deprecated xmapcore R package for data analysis

Filename Version
annmap_homo_sapiens_84.tar.gz (1.11GB) 84
annmap_homo_sapiens_82.tar.gz (1.21GB) 82
annmap_homo_sapiens_78.tar.gz (1.22GB) 78
annmap_homo_sapiens_76.tar.gz (1.26GB) 76
annmap_homo_sapiens_74.tar.gz (1.24GB) 74
annmap_homo_sapiens_72.tar.gz (1.23GB) 72
annmap_homo_sapiens_70.tar.gz (1.23GB) 70
annmap_homo_sapiens_68.tar.gz (1.21GB) 68
xmapcore_homo_sapiens_66.tar.gz (1.17GB) 66
xmapcore_homo_sapiens_64.tar.gz (1.15GB) 64
xmapcore_homo_sapiens_62.tar.gz (1.13GB) 62
xmapcore_homo_sapiens_60.tar.gz (1.12GB) 60
xmapcore_homo_sapiens_58.1.tar.gz (963.1MB) 58
xmapcore_homo_sapiens_56.tar.gz (930.97MB) 56

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annmap Mouse Database

This is the core database for annmap. Annmap is the replacement for the deprecated xmapcore R package for data analysis.

Filename Version
annmap_mus_musculus_84.tar.gz (697.37MB) 84
annmap_mus_musculus_82.tar.gz (737.37MB) 82
annmap_mus_musculus_78.tar.gz (729.1MB) 78
annmap_mus_musculus_76.tar.gz (825.88MB) 76
annmap_mus_musculus_74.tar.gz (717.44MB) 74
annmap_mus_musculus_72.tar.gz (718.17MB) 72
annmap_mus_musculus_70.tar.gz (714.27MB) 70
annmap_mus_musculus_68.tar.gz (713.46MB) 68
xmapcore_mus_musculus_66.tar.gz (679.4MB) 66
xmapcore_mus_musculus_64.tar.gz (671.1MB) 64
xmapcore_mus_musculus_62.tar.gz (665.24MB) 62
xmapcore_mus_musculus_60.tar.gz (654.99MB) 60
xmapcore_mus_musculus_58.1.tar.gz (609.14MB) 58
xmapcore_mus_musculus_56.tar.gz (569.5MB) 56

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annmap Rat Database

This is the core database for annmap. Annmap is the replacement for the deprecated xmapcore R package for data analysis.

Filename Version
annmap_rattus_norvegicus_84.tar.gz (405.16MB) 84
annmap_rattus_norvegicus_82.tar.gz (426.11MB) 82
annmap_rattus_norvegicus_78.tar.gz (403.9MB) 78
annmap_rattus_norvegicus_76.tar.gz (389.14MB) 76
annmap_rattus_norvegicus_74.tar.gz (400.62MB) 74
annmap_rattus_norvegicus_72.tar.gz (400.6MB) 72
annmap_rattus_norvegicus_70.tar.gz (364.98MB) 70
annmap_rattus_norvegicus_68.tar.gz (472.53MB) 68
xmapcore_rattus_norvegicus_66.tar.gz (472.09MB) 66
xmapcore_rattus_norvegicus_64.tar.gz (470.01MB) 64
xmapcore_rattus_norvegicus_62.tar.gz (469.65MB) 62
xmapcore_rattus_norvegicus_60.tar.gz (469.61MB) 60
xmapcore_rattus_norvegicus_58.1.tar.gz (428.29MB) 58
xmapcore_rattus_norvegicus_56.tar.gz (428.68MB) 56

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annmap Pombe Database

This is the core database for annmap. Annmap is the replacement for the deprecated xmapcore R package for data analysis.

Filename Version
annmap_schizosaccharomyces_pombe_31.tar.gz (8.46MB) 31
annmap_schizosaccharomyces_pombe_29.tar.gz (8.93MB) 29
annmap_schizosaccharomyces_pombe_27.tar.gz (8.92MB) 27
annmap_schizosaccharomyces_pombe_21.tar.gz (8.92MB) 21
annmap_schizosaccharomyces_pombe_19.tar.gz (8.92MB) 19
annmap_schizosaccharomyces_pombe_17.tar.gz (8.89MB) 17
annmap_schizosaccharomyces_pombe_15.tar.gz (8.89MB) 15
xmapcore_schizosaccharomyces_pombe_13.tar.gz (8.86MB) 13
xmapcore_schizosaccharomyces_pombe_11.tar.gz (4.72MB) 11
xmapcore_schizosaccharomyces_pombe_9.tar.gz (3.21MB) 9
xmapcore_schizosaccharomyces_pombe_7.tar.gz (3.21MB) 7
xmapcore_schizosaccharomyces_pombe_5.tar.gz (3.2MB) 5
xmapcore_schizosaccharomyces_pombe_4.tar.gz (3.19MB) 4
xmapcore_schizosaccharomyces_pombe_3.tar.gz (3.06MB) 3

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annmap Cerevisiae Database

This is the core database for annmap. Annmap is the replacement for the deprecated xmapcore R package for data analysis.

Filename Version
annmap_saccharomyces_cerevisiae_31.tar.gz (9.2MB) 31
annmap_saccharomyces_cerevisiae_29.tar.gz (9.2MB) 29
annmap_saccharomyces_cerevisiae_27.tar.gz (9.19MB) 27
annmap_saccharomyces_cerevisiae_21.tar.gz (9.12MB) 21
annmap_saccharomyces_cerevisiae_19.tar.gz (9.07MB) 19
annmap_saccharomyces_cerevisiae_17.tar.gz (9.07MB) 17
annmap_saccharomyces_cerevisiae_15.tar.gz (9.07MB) 15
xmapcore_saccharomyces_cerevisiae_13.tar.gz (9.07MB) 13
xmapcore_saccharomyces_cerevisiae_11.tar.gz (4.35MB) 11
xmapcore_saccharomyces_cerevisiae_9.tar.gz (4.4MB) 9
xmapcore_saccharomyces_cerevisiae_7.tar.gz (4.33MB) 7
xmapcore_saccharomyces_cerevisiae_5.tar.gz (3.95MB) 5
xmapcore_saccharomyces_cerevisiae_4.tar.gz (3.96MB) 4

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Stored Procedure patch for xmapcore v1.2.5+

In v1.2.4 of xmapcore, a bug was discovered with the all.probes, probe.details and probe.to.hit functions. These were not being passed the current arraytype, so would return all probes irrespective of which array they were found on. With a single arraytype (as with v58), this isn't a problem, but as we move to adding more arrays to the system, it becomes an issue.

v1.2.5 of xmapcore addresses this issue, but requires updated stored procedures to be able to work.

I have repackaged the v58 database (denoted by the 58.1 name) so that they include these changed procedures, but if you have already installed the database, I have supplied the procedures here as a separate download

If you see the following when calling any of the above queries;

> all.probes()
Error in mysqlExecStatement(conn, statement, ...) :
RS-DBI driver: (could not run statement: Incorrect number of arguments for PROCEDURE xmapcore_homo_sapiens_56.all_probes; expected 0, got 1)

Then you can install this patch by simply doing

mysql -h HOSTNAME -u USER -p xmapcore_SPECIES_VERSION < procedures.sql

Replacing HOSTNAME, USER, SPECIES and VERSION with values for your particular setup

Filename Version
procedures.sql (72.3KB) 1.2.5

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AnnmapBridge

The AnnmapBridge is an application which stands between an R session and the Annmap website. It allows you to overlay your data as a single or multiple plot directly onto the desired genome.

Filename Version
AnnmapBridge-3.6.1.tar.gz (7.22MB) 3.6.1
AnnmapBridge-3.6.tar.gz (7.22MB) 3.6

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Human Exon CDF

The CDF R metadata packages for Human, Mouse and Rat Exon 1.0 ST microarrays have been created from original Affymetrix ASCII chip description files using the makecdfenv and altcdfenvs BioConductor toolboxes.

All the background and control probesets have been removed. These packages most likely require a 64bit machine to run properly. To install the package, download the relevant tarball, and install with the usual command:

R CMD INSTALL DOWNLOADED_FILE.tar.gz

To attach the CDF to the AffyBatch object:

R> my.affy.batch@cdfName <- "DOWNLOADED_FILE"

Filename Version
exon.pmcdf_1.1.tar.gz (26.09MB) 1.1
exon.pmcdf.tar.gz (26.09MB) 1.0

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Mouse Exon CDF

See the Homo Sapiens CDF for a full description

Filename Version
mouseexonpmcdf_1.1.R3.0.tar.gz (22.21MB) 1.1.R3.0
mouseexonpmcdf_1.1.tar.gz (22.18MB) 1.1
mouseexonpmcdf.tar.gz (22.18MB) 1.0

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Rat Exon CDF

See the Human CDF for a full description

Filename Version
ratexonpmcdf_1.1.tar.gz (18.82MB) 1.1

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Old "exonmap" Human Database

Homo Sapiens database for the exonmap R package.

Please note: The exonmap package is being deprecated in favor of the new xmapcore package. Please consider upgrading, as we will soon stop generating these databases

Filename Version
xmap_homo_sapiens_core_62_37g.tgz (675.11MB) 62
xmap_homo_sapiens_core_60_37e.tgz (661.53MB) 60
xmap_homo_sapiens_core_58_37c.tgz (653.02MB) 58
xmap_homo_sapiens_core_56_37a.tgz (595.66MB) 56
xmap_homo_sapiens_core_52_36n.tgz (541.08MB) 52
xmap_homo_sapiens_core_50_36l.tgz (558.93MB) 50
xmap_homo_sapiens_core_47_36i.tgz (552.83MB) 47
xmap_homo_sapiens_core_45_36g.tgz (543.77MB) 45

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Old "exonmap" Mouse Database

Mus Musculus database for the exonmap R package.

Please note: The exonmap package is being deprecated in favor of the new xmapcore package. Please consider upgrading, as we will soon stop generating these databases

Filename Version
xmap_mus_musculus_core_62_37o.tgz (443.2MB) 62
xmap_mus_musculus_core_60_37m.tgz (417.33MB) 60
xmap_mus_musculus_core_58_37k.tgz (414.79MB) 58
xmap_mus_musculus_core_56_37i.tgz (388.43MB) 56
xmap_mus_musculus_core_52_37e.tgz (388.43MB) 52
xmap_mus_musculus_core_50_37c.tgz (401.8MB) 50
xmap_mus_musculus_core_47_37.tgz (399.06MB) 47
xmap_mus_musculus_core_45_36f.tgz (432.89MB) 45

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Old "exonmap" Rat Database

Rattus Norvegicus database for the exonmap R package.

Please note: The exonmap package is being deprecated in favor of the new xmapcore package. Please consider upgrading, as we will soon stop generating these databases

Filename Version
xmap_rattus_norvegicus_core_62_34d.tgz (390.16MB) 62
xmap_rattus_norvegicus_core_60_34b.tgz (388.75MB) 60
xmap_rattus_norvegicus_core_58_34z.tgz (388.76MB) 58
xmap_rattus_norvegicus_core_56_34x.tgz (390.37MB) 56
xmap_rattus_norvegicus_core_52_34u.tgz (286.38MB) 52
xmap_rattus_norvegicus_core_50_34t.tgz (299.12MB) 50
xmap_rattus_norvegicus_core_47_34q.tgz (294.87MB) 47
xmap_rattus_norvegicus_core_45_34o.tgz (293.21MB) 45

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