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software [2014/04/18 10:58] xhx [PyLOH] |
software [2015/05/08 15:06] (current) xhx [MDOS] |
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| ==== PyLOH ==== | ==== PyLOH ==== | ||
| PyLOH is a tool for discovering copy number variations in cancer genomes. PyLOH is available at | PyLOH is a tool for discovering copy number variations in cancer genomes. PyLOH is available at | ||
| - | [[https://github.com/uci-cbcl/PyLOH] | + | [[https://github.com/uci-cbcl/PyLOH]] |
| - | ==== TEMP ==== | + | |
| - | TEMP is a tool for transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data. TEMP is available at [[https://github.com/uci-cbcl/TEMT]] | + | |
| + | ==== TEMP ==== | ||
| + | A tool for transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data, available at [[https://github.com/uci-cbcl/TEMT]] | ||
| + | ==== GBMCI ==== | ||
| + | GBMCI is a tool for survival analysis by direct concordance index learning using gradient boosting, available at [[https://github.com/uci-cbcl/GBMCI]] | ||
| ==== AREM ==== | ==== AREM ==== | ||
| AREM is a tool for ChIP-seq analysis, and is able to discover peaks in repeat regions of the genomes. AREM is available at [[software/arem | Aligning Reads from ChIP-seq data by expectation-maximization ]] | AREM is a tool for ChIP-seq analysis, and is able to discover peaks in repeat regions of the genomes. AREM is available at [[software/arem | Aligning Reads from ChIP-seq data by expectation-maximization ]] | ||
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| ==== MDOS ==== | ==== MDOS ==== | ||
| - | [[http://www.ics.uci.edu/~xhx/project/mdos | MDOS]] motif discovery using orthologous sequences (alignment independent) | ||
| + | [[https://github.com/uci-cbcl/mdos|MDOS]] motif discovery using orthologous sequences (alignment independent) | ||
| ==== iPubMed ==== | ==== iPubMed ==== | ||