Index:
- annmap Human Database
- annmap Mouse Database
- annmap Rat Database
- annmap Pombe Database
- annmap Cerevisiae Database
- Stored Procedure patch for xmapcore v1.2.5+
- XMapBridge
- Human Exon CDF
- Mouse Exon CDF
- Rat Exon CDF
- Old "exonmap" Human Database
- Old "exonmap" Mouse Database
- 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_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 |
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_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 |
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_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 |
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_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 |
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_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 |
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 |
XMapBridge
The X:Map Bridge 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.
There are 2 parts to the XMapBridge, this Java part and an R library which can be found on the Bioconductor site.
(Without the R package, this Java part will just run in demo mode)
| Filename | Version | |
|---|---|---|
| XMapBridge3.0.tar.gz (6.33MB) | 3.0 |
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 |
Mouse Exon CDF
See the Homo Sapiens CDF for a full description
| Filename | Version | |
|---|---|---|
| mouseexonpmcdf_1.1.tar.gz (22.18MB) | 1.1 | |
| mouseexonpmcdf.tar.gz (22.18MB) | 1.0 |
Rat Exon CDF
See the Human CDF for a full description
| Filename | Version | |
|---|---|---|
| ratexonpmcdf_1.1.tar.gz (18.82MB) | 1.1 |
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 |
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 |
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 |