wiki.chasmsoftware.org

Main Page - Chasm Software Wiki

From Chasm Software Wiki. Welcome to the Karchinlab CHASM wiki. Here you will find information on the following software packages:. Utations) is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. Patch v1 for CHASM 3.0 and VEST 3.0 has been released. See Downloads. About Chasm Softwar...

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From Chasm Software Wiki. Welcome to the Karchinlab CHASM wiki. Here you will find information on the following software packages:. Utations) is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. Patch v1 for CHASM 3.0 and VEST 3.0 has been released. See Downloads. About Chasm Softwar...

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10 about our software

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Main Page - Chasm Software Wiki | wiki.chasmsoftware.org Reviews

https://wiki.chasmsoftware.org

From Chasm Software Wiki. Welcome to the Karchinlab CHASM wiki. Here you will find information on the following software packages:. Utations) is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. Patch v1 for CHASM 3.0 and VEST 3.0 has been released. See Downloads. About Chasm Softwar...

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wiki.chasmsoftware.org

1

SNVBox Overview - Chasm Software Wiki

http://wiki.chasmsoftware.org/index.php/SNVBox_Overview

From Chasm Software Wiki. SNVBox is a database of features precomputed for every codon in expressed human transcripts contained in the Refseq, CCDS and Ensembl databases. It allows rapid retrieval of features for very large datasets of missense variants. Features can be retrieved from the SNVBox database using either transcript, amino acid substitution and codon position, or genomic coordinates on the GRCh37/hg19 human genome assembly. Amino Acid Substitution features. About Chasm Software Wiki.

2

SoftwareLicense - Chasm Software Wiki

http://wiki.chasmsoftware.org/index.php/SoftwareLicense

From Chasm Software Wiki. JHU Academic Software License Agreement. This license agreement ("License"), effective automatically by and between you (hereinafter referred to as the "Licensee") and The Johns Hopkins University ( JHU ) for use of the software known as CHASM (the Software ) once and only so long as Licensee complies with the following terms and conditions:. Licensee agrees that it will use the Software, and any modifications, improvements, or derivatives to the Software that the Licensee may c...

3

Mailing list - Chasm Software Wiki

http://wiki.chasmsoftware.org/index.php/Mailing_list

From Chasm Software Wiki. To join our mailing list, please do one of the following:. 1) If you are a Hopkins Affiliate with a JHED account:. Go to https:/ lists.johnshopkins.edu/sympa/subscribe/chasm-users. And click on the Subscribe link under List Operations. Please send an email to sympa@lists.johnshopkins.edu with the following in the subject line (substituting your actual email address):. SUBSCRIBE chasm-users YOUR EMAIL ADDRESS. This page was last modified on 8 August 2011, at 20:58.

4

CHASM Tutorial - Chasm Software Wiki

http://wiki.chasmsoftware.org/index.php/CHASM_Tutorial

From Chasm Software Wiki. Passenger Mutation Rate Tables. Cancer-specific passenger mutation rate table. Passenger mutation rates are estimated based on mutation frequencies in eight di-nucleotide contexts. The passenger mutation rate table is a tab delimited text file in the following format:. The asterisk indicates the mutated base in the di-nucleotide contexts. We recommend building a passenger rate table based on your own mutation data. A suggested protocol is provided here. If the list of mutations ...

5

ReleaseHistory - Chasm Software Wiki

http://wiki.chasmsoftware.org/index.php/ReleaseHistory

From Chasm Software Wiki. 03/05/2014 - CHASM 3.0. Classifiers were retrained with SNVBox 3.0. 03/05/2014 - SNVBox 3.0. Constructed with the latest RefSeq, CCDS, and Ensembl transcripts. 03/05/2014 - VEST 3.0. Updated the VEST training set to use HGMD2013v4 release. The classifier was retrained with SNVBox 3.0. 09/19/2013 - CHASM 1.0.8. 26 classifiers are included: 20 context tables estimated from TCGA sequencing studies, 4 from ICGC studies, 1 from Johns Hopkins (Velculescu/Kinzler/Vogelstein lab), and 1...

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From Chasm Software Wiki. Welcome to the Karchinlab CHASM wiki. Here you will find information on the following software packages:. Utations) is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage. Patch v1 for CHASM 3.0 and VEST 3.0 has been released. See Downloads. About Chasm Softwar...

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