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software [2013/10/17 22:03] xhx [AREM] |
software [2015/05/08 15:06] 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 ==== | ||
- | [[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]]. | + | ==== Hobbes ==== |
+ | Hobbes is a tool for very fast, very accurate short-read sequence alignment. Hobbes has its own [[http://hobbes.ics.uci.edu/ | homepage]]. | ||
- | ===== Software ===== | + | ==== Genomix ==== |
- | | **Note:** Most software published by our group is also available on [[https://github.com/uci-cbcl | github.com/uci-cbcl]]| | + | Parallel genome assembly using Hyracks, available at [[https://github.com/uci-cbcl/genomix|https://github.com/uci-cbcl/genomix]] |
- | ==== Hobbes ==== | + | ==== EXTREME ==== |
- | Hobbes is a tool for very fast, very accurate short-read sequence alignment. Hobbes has its own [[http://hobbes.ics.uci.edu/ | homepage]]. | + | 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 is a tool for discovering copy number variations in cancer genomes. PyLOH is available at | ||
+ | [[https://github.com/uci-cbcl/PyLOH]] | ||
==== 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]]. | ||
+ |