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software [2015/05/08 15:06] (current) xhx [MDOS] |
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| - | ====== Servers ====== | + | | **Note:** Most software published by our group is also available on [[https://github.com/uci-cbcl | github.com/uci-cbcl]]| |
| - | ==== iPubMed ==== | ||
| - | [[http://ipubmed.ics.uci.edu | iPubMed]]: instant PubMed, featuring interactive and fuzzy search | ||
| - | ==== MotifMap ==== | + | ==== Hobbes ==== |
| - | [[http://motifmap.ics.uci.edu | MotifMap]]: A comprehensive map of regulatory motif sites in human and model organisms. | + | Hobbes is a tool for very fast, very accurate short-read sequence alignment. Hobbes has its own [[http://hobbes.ics.uci.edu/ | homepage]]. |
| - | An older version of MotifMap, as published in our first paper and specific to the human dataset is available at [[http://www.ics.uci.edu/~xhx/project/MotifMap]]. | + | ==== Genomix ==== |
| - | ======= Software ======= | + | 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]] | ||
| - | | **Note:** Most software published by our group is also available on [[https://github.com/uci-cbcl | github.com/uci-cbcl]]| | + | ==== PyLOH ==== |
| - | + | PyLOH is a tool for discovering copy number variations in cancer genomes. PyLOH is available at | |
| - | ==== Hobbes ==== | + | [[https://github.com/uci-cbcl/PyLOH]] |
| - | Hobbes is a tool for very fast, very accurate short-read sequence alignment. Hobbes has its own [[http://hobbes.ics.uci.edu/ | homepage]]. | + | |
| ==== TEMP ==== | ==== TEMP ==== | ||
| - | TEMP is a tool for transcripts abundances estimation from heterogeneous tissue sample of RNA-Seq data, and 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 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 ]] | ||
| ==== tree-hmm ==== | ==== tree-hmm ==== | ||
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| Code is available at [[https://github.com/uci-cbcl/tree-hmm]] and some sample data is available at [[http://cbcl.ics.uci.edu/public_data/tree-hmm-sample-data]] | Code is available at [[https://github.com/uci-cbcl/tree-hmm]] and some sample data is available at [[http://cbcl.ics.uci.edu/public_data/tree-hmm-sample-data]] | ||
| - | ==== AREM ==== | ||
| - | AREM is a tool for ChIP-seq analysis, and is designed to be able to discover peaks in repeat regions of the genomes. The software is available at [[software/arem | Aligning Reads from ChIP-seq data by expectation-maximization ]] | ||
| ==== SGD-RJ ==== | ==== SGD-RJ ==== | ||
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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 ==== | ||
| + | [[http://ipubmed.ics.uci.edu | iPubMed]]: instant PubMed, featuring interactive and fuzzy search | ||
| + | |||
| + | ==== MotifMap ==== | ||
| + | [[http://motifmap.ics.uci.edu | MotifMap]]: A comprehensive map of regulatory motif sites in human and model organisms. | ||
| + | |||
| + | An older version of MotifMap, as published in our first paper and specific to the human dataset is available at [[http://www.ics.uci.edu/~xhx/project/MotifMap]]. | ||
| + | |||