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software [2013/10/17 22:04]
xhx
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.eduhomepage]].
  
-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]]
  
-|  **Note:​** ​ Most software published by our group is also available ​on [[https://​github.com/​uci-cbcl ​| github.com/uci-cbcl]]|+==== 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]]
  
-==== Hobbes ​==== +==== PyLOH ==== 
-Hobbes ​is a tool for very fast, very accurate short-read sequence alignment ​Hobbes has its own [[http://hobbes.ics.uci.edu| homepage]].+PyLOH is a tool for discovering copy number variations in cancer genomesPyLOH 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]]+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]]. 
 + 
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