# This file created by conda-build 3.21.4
# meta.yaml template originally from:
# /opt/recipe, last modified Fri Apr  2 07:52:20 2021
# ------------------------------------------------

package:
  name: bioconductor-moonlightr
  version: 1.16.0
source:
  md5: 62c9d17b32e9e73fe288650323b51a41
  url:
    - https://bioarchive.galaxyproject.org/MoonlightR_1.16.0.tar.gz
    - https://bioconductor.org/packages/3.12/bioc/src/contrib/MoonlightR_1.16.0.tar.gz
    - https://depot.galaxyproject.org/software/bioconductor-moonlightr/bioconductor-moonlightr_1.16.0_src_all.tar.gz
build:
  noarch: generic
  number: '1'
  rpaths:
    - lib/
    - lib/R/lib/
  string: r40hdfd78af_1
requirements:
  build:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 1_gnu
    - kernel-headers_linux-64 2.6.32 h77966d4_13
    - libdrm-cos6-x86_64 2.4.65 h9d98e8f_1104
    - libgcc-ng 9.3.0 h2828fa1_18
    - libgomp 9.3.0 h2828fa1_18
    - libselinux-cos6-x86_64 2.0.94 h9d98e8f_1104
    - libsepol-cos6-x86_64 2.0.41 h9d98e8f_1104
    - libx11-common-cos6-x86_64 1.6.4 h9d98e8f_1104
    - libx11-cos6-x86_64 1.6.4 h9d98e8f_1104
    - libxcb 1.13 h7f98852_1003
    - libxdamage-cos6-x86_64 1.1.3 h9d98e8f_1104
    - libxxf86vm-cos6-x86_64 1.1.3 h9d98e8f_1104
    - mesa-dri-drivers-cos6-x86_64 11.0.7 h9d98e8f_1104
    - mesa-dri1-drivers-cos6-x86_64 7.11 h9d98e8f_1104
    - mesa-libgl-cos6-x86_64 11.0.7 h9d98e8f_1104
    - mesa-libgl-devel-cos6-x86_64 11.0.7 h9d98e8f_1104
    - pthread-stubs 0.4 h36c2ea0_1001
    - sysroot_linux-64 2.12 h77966d4_13
    - xorg-fixesproto 5.0 h14c3975_1002
    - xorg-kbproto 1.0.7 h7f98852_1002
    - xorg-libx11 1.6.12 h516909a_0
    - xorg-libxau 1.0.9 h7f98852_0
    - xorg-libxdmcp 1.1.3 h7f98852_0
    - xorg-libxfixes 5.0.3 h516909a_1004
    - xorg-xextproto 7.3.0 h7f98852_1002
    - xorg-xproto 7.0.31 h7f98852_1007
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 1_gnu
    - _r-mutex 1.0.1 anacondar_1
    - binutils_impl_linux-64 2.35.1 h193b22a_2
    - binutils_linux-64 2.35 h67ddf6f_30
    - bioconductor-annotationdbi 1.52.0 r40hdfd78af_1
    - bioconductor-biobase 2.50.0 r40hd029910_1
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    - bioconductor-biomart 2.46.3 r40hdfd78af_0
    - bioconductor-clusterprofiler 3.18.1 r40hdfd78af_0
    - bioconductor-delayedarray 0.16.3 r40hd029910_0
    - bioconductor-do.db 2.9 r40hdfd78af_10
    - bioconductor-dose 3.16.0 r40hdfd78af_1
    - bioconductor-enrichplot 1.10.2 r40hdfd78af_0
    - bioconductor-fgsea 1.16.0 r40h399db7b_1
    - bioconductor-genomeinfodb 1.26.4 r40hdfd78af_0
    - bioconductor-genomeinfodbdata 1.2.4 r40hdfd78af_1
    - bioconductor-genomicranges 1.42.0 r40hd029910_1
    - bioconductor-geoquery 2.58.0 r40hdfd78af_1
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    - bioconductor-gosemsim 2.16.1 r40h399db7b_0
    - bioconductor-iranges 2.24.1 r40hd029910_0
    - bioconductor-limma 3.46.0 r40hd029910_1
    - bioconductor-matrixgenerics 1.2.1 r40hdfd78af_0
    - bioconductor-qvalue 2.22.0 r40hdfd78af_1
    - bioconductor-s4vectors 0.28.1 r40hd029910_0
    - bioconductor-summarizedexperiment 1.20.0 r40hdfd78af_1
    - bioconductor-tcgabiolinks 2.18.0 r40hdfd78af_1
    - bioconductor-tcgabiolinksgui.data 1.10.0 r40hdfd78af_1
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    - gettext 0.19.8.1 h0b5b191_1005
    - gfortran_impl_linux-64 9.3.0 hc4a2995_18
    - gfortran_linux-64 9.3.0 hdc58fab_30
    - gmp 6.2.1 h58526e2_0
    - graphite2 1.3.13 h58526e2_1001
    - gsl 2.6 he838d99_2
    - gxx_impl_linux-64 9.3.0 hd87eabc_18
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    - libstdcxx-devel_linux-64 9.3.0 hb016644_18
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    - libxml2 2.9.10 h72842e0_3
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    - make 4.3 hd18ef5c_1
    - ncurses 6.2 h58526e2_4
    - openssl 1.1.1k h7f98852_0
    - pango 1.48.4 hb8ff022_0
    - pcre 8.44 he1b5a44_0
    - pcre2 10.36 h032f7d1_1
    - pixman 0.40.0 h36c2ea0_0
    - pthread-stubs 0.4 h36c2ea0_1001
    - r-askpass 1.1 r40hcdcec82_2
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    - r-base 4.0.3 h349a78a_8
    - r-base64enc 0.1_3 r40hcdcec82_1004
    - r-bh 1.75.0_0 r40hc72bb7e_0
    - r-biocmanager 1.30.12 r40hc72bb7e_0
    - r-bit 4.0.4 r40hcdcec82_0
    - r-bit64 4.0.5 r40hcdcec82_0
    - r-bitops 1.0_6 r40hcdcec82_1004
    - r-blob 1.2.1 r40h6115d3f_1
    - r-brio 1.1.1 r40hcfec24a_0
    - r-bslib 0.2.4 r40hc72bb7e_0
    - r-cachem 1.0.4 r40hcfec24a_0
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    - r-circlize 0.4.12 r40hc72bb7e_0
    - r-cli 2.3.1 r40hc72bb7e_0
    - r-clipr 0.7.1 r40h142f84f_0
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    - r-digest 0.6.27 r40h1b71b39_0
    - r-doparallel 1.0.16 r40h142f84f_0
    - r-downloader 0.4 r40h6115d3f_1003
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    - r-evaluate 0.14 r40h6115d3f_2
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    - r-fastmap 1.1.0 r40h03ef668_0
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    - r-fs 1.5.0 r40h0357c0b_0
    - r-futile.logger 1.4.3 r40h6115d3f_1003
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    - r-globaloptions 0.1.2 r40_0
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    - r-graphlayouts 0.7.1 r40h1b71b39_0
    - r-gridextra 2.3 r40h6115d3f_1003
    - r-gtable 0.3.0 r40h6115d3f_3
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    - r-igraph 1.2.6 r40hfbf21e4_1
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    - r-rcolorbrewer 1.1_2 r40h6115d3f_1003
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    - r-shadowtext 0.0.7 r40h6115d3f_1
    - r-shape 1.4.5 r40_0
    - r-shiny 1.6.0 r40hc72bb7e_0
    - r-snow 0.4_3 r40h6115d3f_1002
    - r-sourcetools 0.1.7 r40he1b5a44_1002
    - r-stringi 1.5.3 r40hcabe038_1
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    - r-vctrs 0.3.7 r40hcfec24a_0
    - r-viridis 0.5.1 r40h6115d3f_1004
    - r-viridislite 0.3.0 r40h6115d3f_1003
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    - r-xml2 1.3.2 r40h0357c0b_1
    - r-xtable 1.8_4 r40h6115d3f_3
    - r-yaml 2.2.1 r40hcfec24a_1
    - r-zeallot 0.1.0 r40h6115d3f_1002
    - readline 8.0 he28a2e2_2
    - sed 4.8 he412f7d_0
    - sysroot_linux-64 2.12 h77966d4_13
    - tk 8.6.10 h21135ba_1
    - tktable 2.10 hb7b940f_3
    - xorg-kbproto 1.0.7 h7f98852_1002
    - xorg-libice 1.0.10 h7f98852_0
    - xorg-libsm 1.2.3 hd9c2040_1000
    - xorg-libx11 1.7.0 h7f98852_0
    - xorg-libxau 1.0.9 h7f98852_0
    - xorg-libxdmcp 1.1.3 h7f98852_0
    - xorg-libxext 1.3.4 h7f98852_1
    - xorg-libxrender 0.9.10 h7f98852_1003
    - xorg-libxt 1.2.1 h7f98852_2
    - xorg-renderproto 0.11.1 h7f98852_1002
    - xorg-xextproto 7.3.0 h7f98852_1002
    - xorg-xproto 7.0.31 h7f98852_1007
    - xz 5.2.5 h516909a_1
    - zlib 1.2.11 h516909a_1010
    - zstd 1.4.9 ha95c52a_0
  run:
    - bioconductor-biobase >=2.50.0,<2.51.0
    - bioconductor-clusterprofiler >=3.18.0,<3.19.0
    - bioconductor-dose >=3.16.0,<3.17.0
    - bioconductor-geoquery >=2.58.0,<2.59.0
    - bioconductor-limma >=3.46.0,<3.47.0
    - bioconductor-summarizedexperiment >=1.20.0,<1.21.0
    - bioconductor-tcgabiolinks >=2.18.0,<2.19.0
    - r-base >=4.0,<4.1.0a0
    - r-circlize
    - r-doparallel
    - r-foreach
    - r-gplots
    - r-hiver
    - r-parmigene
    - r-randomforest
    - r-rcolorbrewer
    - r-rismed
test:
  commands:
    - LD_LIBRARY_PATH="${BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64:${BUILD_PREFIX}/lib"
      $R -e "library('MoonlightR')"
about:
  description: 'Motivation: The understanding of cancer mechanism requires the identification
    of genes playing a role in the development of the pathology and the characterization
    of their role (notably oncogenes and tumor suppressors). Results: We present an
    R/bioconductor package called MoonlightR which returns a list of candidate driver
    genes for specific cancer types on the basis of TCGA expression data. The method
    first infers gene regulatory networks and then carries out a functional enrichment
    analysis (FEA) (implementing an upstream regulator analysis, URA) to score the
    importance of well-known biological processes with respect to the studied cancer
    type. Eventually, by means of random forests, MoonlightR predicts two specific
    roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii)
    oncogenes (OCGs). As a consequence, this methodology does not only identify genes
    playing a dual role (e.g. TSG in one cancer type and OCG in another) but also
    helps in elucidating the biological processes underlying their specific roles.
    In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer
    type. This may help in answering the question whether some genes change role between
    early stages (I, II) and late stages (III, IV) in breast cancer. In the future,
    this analysis could be useful to determine the causes of different resistances
    to chemotherapeutic treatments.'
  home: https://bioconductor.org/packages/3.12/bioc/html/MoonlightR.html
  license: GPL (>= 3)
  license_file: /opt/conda/conda-bld/bioconductor-moonlightr_1617353614313/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/lib/R/share/licenses/GPL-3
  summary: Identify oncogenes and tumor suppressor genes from omics data
extra:
  container:
    extended-base: true
  copy_test_source_files: true
  final: true
