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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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Main Page - Chasm Software Wiki | chasmsoftware.org Reviews

https://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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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...

INTERNAL PAGES

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1

CHASM Tutorial - Chasm Software Wiki

http://www.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 ...

2

SNVBox Overview - Chasm Software Wiki

http://www.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.

3

Publications - Chasm Software Wiki

http://www.chasmsoftware.org/index.php/Publications

From Chasm Software Wiki. Wong WC, Kim D, Carter H, Diekhans M, Ryan M and Karchin R (2011) CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer Bioinformatics. 27(15):2147-8 PubMed. Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, Karchin R.(2009) Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.Cancer Research. 69(16):6660-7 PubMed. Bozic I, Antal T, Ohts...

4

CHASM DL - Chasm Software Wiki

http://www.chasmsoftware.org/index.php/CHASM_DL

From Chasm Software Wiki. SNVBox Feature Retrieval Tool. The following download package includes CHASM and the latest CHASM Classifier Pack. MD5 Checksum: 04bd301d3d90b84e60f1e2dd2b41477c ). MD5 Checksum: 0c2c2ebf26c08e02eacaa2044e4aad76 ). To inspect the checksum:. Md5sum CHASM64DL.3.0.tar.gz md5sum CHASM32DL.3.0.tar.gz. The following download package includes VEST and the latest VEST Classifier Pack. MD5 Checksum: c04852243fd4b820b6cb0e2eb52cad1b ). MD5 Checksum: 64bc449df8575353e83c32abfcf6ff69 ).

5

CHASM update - Chasm Software Wiki

http://www.chasmsoftware.org/index.php/CHASM_update

From Chasm Software Wiki. To keep up to date with the latest developments, CHASM Classifier Pack and SNV-Box MySQL Database needs to be downloaded and updated regularly. Updating CHASM Classifier Pack. The CHASM Classifier Pack is updated periodically. The latest Classifier Pack and extract this on top of the (installation location)/CHASM/ClassifierPack. Tar xvzf (some file name) (Overwrite! The SNV-Box database is updated on a weekly basis. The latest SNV-Box MySQL Database. About Chasm Software Wiki.

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The Chasms of the Earth. If in doubt, it's probably an anagram. Saturday, December 22, 2007. Back, but not for long. I can't imagine that anyone will read this, although maybe one or two long-dormant RSS feeds will leap into life, but anyway, I just need to record something that I've only just discovered:. The Louvre Pyramid does not. Contain precisely 666 panes of glass. Posted by Tim Footman at 4:05 pm. Thursday, June 14, 2007. Oh, and if you'll just allow me the luxury of a BIG PLOT SPOILER. And now w...

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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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Music | Chasms

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