From Chasm Software Wiki
Contents |
CHASM Install Pack
Current version: 3.0
The following download package includes CHASM and the latest CHASM Classifier Pack.
CHASM 64-bit (MD5 Checksum: 04bd301d3d90b84e60f1e2dd2b41477c )
CHASM 32-bit (MD5 Checksum: 0c2c2ebf26c08e02eacaa2044e4aad76 )
To inspect the checksum:
> md5sum CHASM64DL.3.0.tar.gz > md5sum CHASM32DL.3.0.tar.gz
Patch v1
If you downloaded CHASM before 05/22/2014, your CHASM package contains a bug that prevents getting CHASM scores for a small portion of the codons in the human genome. We recommend your applying this patch: CHASM 3.0 patch v1
(Last updated 2014/05/22)
VEST Install Pack
Current version: 3.0
Sep 15, 2016 Minor-bug fix: replaced an unreachable hard-coded database connection in config file. If you have been using VEST 3.0 without a problem, there is no need to download it again.
The following download package includes VEST and the latest VEST Classifier Pack.
VEST 64-bit (MD5 Checksum: c04852243fd4b820b6cb0e2eb52cad1b )
VEST 32-bit (MD5 Checksum: 64bc449df8575353e83c32abfcf6ff69 )
To inspect the checksum:
> md5sum VEST64DL.3.0.tar.gz > md5sum VEST32DL.3.0.tar.gz
Patch v1
If you downloaded VEST before 05/22/2014, your VEST package contains a bug that prevents getting VEST scores for a small portion of the codons in the human genome. We recommend your applying this patch: VEST 3.0 patch v1
(Last updated 2014/05/22)
SNVBox Feature Retrieval Tool
Current version: 3.0
The following download package contains code to retrieve features from the SNVBox database.
(MD5 Checksum: 786a0cac1b1b7a2c53a79ef5b5a96be4 )
(Last updated 2014/05/22)
Classifier Pack Updates
Current version: 3.0
The Classifier Pack contains supporting files used to generate training sets of driver and putative passenger mutations. These supporting files are periodically updated. We suggest that you always use the latest version. To update the Classifier Pack, simply download the file and replace the /CHASM/ClassifierPack folder.
(MD5 Checksum: 5494ea123335b276fcfa02b1e0bbba8d )
(Last updated 2014/05/22)
SNVBox MySQL Database
Current version: 3.0
The SNVBox database contains the precomputed features used by CHASM and VEST. Please download and follow the installation instructions to set up/update your database. IMPORTANT -- if you update your Classifier Pack, make sure you have the most up-to-date version of SNVBox.
(MD5 Checksum: 6b410f0c63cb6d3f5ecbb7642c3f731a )
(Last updated 2014/03/05)
PARF Source Code
Current version: 3.0
PARF is a Random Forest software package, written in Fortran 90, by Goran Topic and Tomislav Smuc at Rudjer Boskovic Institute in Croatia. It is distributed under the GNU GPL v2 license. For more information, see PARF at Google Code.
(MD5 Checksum: 0785407c45258228bf7dc21ed9c489e6 )
(Last updated 2013/05/22)
