CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.
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DOI：
10.1093/bioinformatics/btr357
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发表时间：
2011-08-01
期刊：
影响因子：
--
通讯作者：
Karchin R
中科院分区：
文献类型：
--
作者：
Wong WC;Kim D;Carter H;Diekhans M;Ryan MC;Karchin R
Summary: Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. Availability and Implementation: MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM. Contact: karchin@jhu.edu Supplementary Information: Supplementary data are available at Bioinformatics online.
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DOI：
10.1038/nrc1299
发表时间：
2004-03
期刊：
Nature reviews. Cancer
影响因子：
--
作者：
通讯作者：
--
影响因子：
11.2
作者：
Carter H;Chen S;Isik L;Tyekucheva S;Velculescu VE;Kinzler KW;Vogelstein B;Karchin R
通讯作者：
Karchin R
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
3.6
作者：
Carter, Hannah;Samayoa, Josue;Karchin, Rachel
通讯作者：
Karchin, Rachel
影响因子：
9.5
作者：
Karchin, Rachel
通讯作者：
Karchin, Rachel