Mercurial > repos > iuc > package_monocle_1_0_0

annotate tool_dependencies.xml @ 2:ba0bc7c7954e draft default tip

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planemo upload commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
author iuc
date Fri, 09 Oct 2015 05:23:22 -0400
parents 827847c48138
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R" version="3.1.2">
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4 <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="monocle" version="1.0.0">
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7 <install version="1.0">
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8 <actions>
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9 <action type="setup_r_environment">
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10 <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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11 <package name="R" version="3.1.2" />
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12 </repository>
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13 <package>https://github.com/bgruening/download_store/raw/master/monocle/VGAM_0.9-6.tar.gz</package>
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14 <package>https://github.com/bgruening/download_store/raw/master/monocle/HSMMSingleCell_1.0.0.tar.gz</package>
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15 <package>https://github.com/bgruening/download_store/raw/master/monocle/BiocGenerics_0.12.1.tar.gz</package>
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16 <package>https://github.com/bgruening/download_store/raw/master/monocle/Biobase_2.26.0.tar.gz</package>
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17 <package>https://github.com/bgruening/download_store/raw/master/monocle/Rcpp_0.11.4.tar.gz</package>
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18 <package>https://github.com/bgruening/download_store/raw/master/monocle/plyr_1.8.1.tar.gz</package>
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19 <package>https://github.com/bgruening/download_store/raw/master/monocle/digest_0.6.8.tar.gz</package>
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20 <package>https://github.com/bgruening/download_store/raw/master/monocle/gtable_0.1.2.tar.gz</package>
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21 <package>https://github.com/bgruening/download_store/raw/master/monocle/stringr_0.6.2.tar.gz</package>
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22 <package>https://github.com/bgruening/download_store/raw/master/monocle/reshape2_1.4.1.tar.gz</package>
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23 <package>https://github.com/bgruening/download_store/raw/master/monocle/RColorBrewer_1.1-2.tar.gz</package>
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24 <package>https://github.com/bgruening/download_store/raw/master/monocle/dichromat_2.0-0.tar.gz</package>
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25 <package>https://github.com/bgruening/download_store/raw/master/monocle/colorspace_1.2-4.tar.gz</package>
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26 <package>https://github.com/bgruening/download_store/raw/master/monocle/munsell_0.4.2.tar.gz</package>
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27 <package>https://github.com/bgruening/download_store/raw/master/monocle/labeling_0.3.tar.gz</package>
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28 <package>https://github.com/bgruening/download_store/raw/master/monocle/scales_0.2.4.tar.gz</package>
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29 <package>https://github.com/bgruening/download_store/raw/master/monocle/proto_0.3-10.tar.gz</package>
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30 <package>https://github.com/bgruening/download_store/raw/master/monocle/MASS_7.3-39.tar.gz</package>
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31 <package>https://github.com/bgruening/download_store/raw/master/monocle/ggplot2_1.0.0.tar.gz</package>
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32 <package>https://github.com/bgruening/download_store/raw/master/monocle/lattice_0.20-30.tar.gz</package>
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33 <package>https://github.com/bgruening/download_store/raw/master/monocle/Matrix_1.1-5.tar.gz</package>
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34 <package>https://github.com/bgruening/download_store/raw/master/monocle/igraph_0.7.1.tar.gz</package>
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35 <package>https://github.com/bgruening/download_store/raw/master/monocle/cluster_2.0.1.tar.gz</package>
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36 <package>https://github.com/bgruening/download_store/raw/master/monocle/combinat_0.0-8.tar.gz</package>
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37 <package>https://github.com/bgruening/download_store/raw/master/monocle/fastICA_1.2-0.tar.gz</package>
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38 <package>https://github.com/bgruening/download_store/raw/master/monocle/irlba_1.0.3.tar.gz</package>
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39 <package>https://github.com/bgruening/download_store/raw/master/monocle/matrixStats_0.14.0.tar.gz</package>
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40 <package>https://github.com/bgruening/download_store/raw/master/monocle/limma_3.22.4.tar.gz</package>
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41 <package>https://github.com/bgruening/download_store/raw/master/monocle/monocle_1.0.0.tar.gz</package>
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42 </action>
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43 </actions>
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44 </install>
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45 <readme>
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46 Analysis tools for single-cell expression experiments.
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47
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48 Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to
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49 progress through a biological process, without knowing ahead of time which genes define progress through that process.
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50 Monocle also performs differential expression analysis, clustering, visualization,
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51 and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.
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52
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53 Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS and Rinn JL (2014). “The dynamics and regulators of cell fate decisions are revealed by pseudo-temporal ordering of single cells.” Nature Biotechnology.
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54
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55 http://www.bioconductor.org/packages/release/bioc/html/monocle.html
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56
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57 </readme>
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58 </package>
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59 </tool_dependency>