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software [2015/11/24 19:23]
cassa
software [2018/02/03 18:34] (current)
dweghorn
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   * [[http://​genetics.bwh.harvard.edu/​snptrack|SNPtrack]] is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.   * [[http://​genetics.bwh.harvard.edu/​snptrack|SNPtrack]] is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.
   * [[http://​genetics.bwh.harvard.edu/​scone/​|SCONE]] is a tool for predicting the effect of noncoding variation on regulatory sequences based on evolutionary conservation. It is available for download as a standalone application.   * [[http://​genetics.bwh.harvard.edu/​scone/​|SCONE]] is a tool for predicting the effect of noncoding variation on regulatory sequences based on evolutionary conservation. It is available for download as a standalone application.
 +  * [[http://​genetics.bwh.harvard.edu/​pines/​|PINES]] (Phenotype-Informed Noncoding Element Scoring) evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations,​ utilizing genomic annotations most relevant to phenotypes of interest.
  
 ===Tools for Mass Spectrometry and Proteomics=== ===Tools for Mass Spectrometry and Proteomics===
   * [[http://​genetics.bwh.harvard.edu/​cgi-bin/​msfilter/​eagleeye.cgi|EagleEye]] is a tool for filtering noise and background proteins from LC-MS/MS spectra. It is available as a web service.   * [[http://​genetics.bwh.harvard.edu/​cgi-bin/​msfilter/​eagleeye.cgi|EagleEye]] is a tool for filtering noise and background proteins from LC-MS/MS spectra. It is available as a web service.
   * [[http://​genetics.bwh.harvard.edu/​msblast|MS-BLAST]] is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service.   * [[http://​genetics.bwh.harvard.edu/​msblast|MS-BLAST]] is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service.
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 +===Tools for Statistical Genetics===
 +  * [[ JLIM ]] is a tool to test for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study. ​
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 +===Tools for Cancer Genomics===
 +  * [[ http://​genetics.bwh.harvard.edu/​cbase/​index.html|CBaSE ]] enables cancer type and gene-specific estimation of the strength of negative and positive selection. It is available as a browser-based tool as well as for download as a standalone package.
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