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software [2013/10/17 22:13] xhx |
software [2015/05/08 15:06] (current) xhx [MDOS] |
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==== Genomix ==== | ==== Genomix ==== | ||
- | Genomix is parallel sof, available at [[https://github.com/uci-cbcl/genomix]] | + | |
+ | Parallel genome assembly using Hyracks, available at [[https://github.com/uci-cbcl/genomix|https://github.com/uci-cbcl/genomix]] | ||
+ | |||
+ | ==== EXTREME ==== | ||
+ | An online EM implementation of the MEME model for fast motif discovery in large ChIP-Seq and DNase-Seq Footprinting data, available at [[https://github.com/uci-cbcl/EXTREME]] | ||
==== PyLOH ==== | ==== PyLOH ==== | ||
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==== TEMP ==== | ==== 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]] | + | 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 ==== |