# This file created by conda-build 3.18.9
# meta.yaml template originally from:
# /opt/recipe, last modified Mon Aug  5 15:41:58 2019
# ------------------------------------------------

package:
    name: bioconductor-dep
    version: 1.6.0
source:
    md5: e28b75342a72f73f471ecd755df87539
    url:
        - https://bioarchive.galaxyproject.org/DEP_1.6.0.tar.gz
        - https://bioconductor.org/packages/3.9/bioc/src/contrib/DEP_1.6.0.tar.gz
        - https://depot.galaxyproject.org/software/bioconductor-dep/bioconductor-dep_1.6.0_src_all.tar.gz
build:
    noarch: generic
    number: '1'
    rpaths:
        - lib/
        - lib/R/lib/
    string: r36_1
requirements:
    host:
        - _libgcc_mutex 0.1 main
        - _r-mutex 1.0.1 anacondar_1
        - binutils_impl_linux-64 2.31.1 h6176602_1
        - binutils_linux-64 2.31.1 h6176602_7
        - bioconductor-affy 1.62.0 r36h516909a_1
        - bioconductor-affyio 1.54.0 r36h516909a_1
        - bioconductor-biobase 2.44.0 r36h516909a_1
        - bioconductor-biocgenerics 0.30.0 r36_1
        - bioconductor-biocparallel 1.18.0 r36he1b5a44_1
        - bioconductor-complexheatmap 2.0.0 r36_1
        - bioconductor-delayedarray 0.10.0 r36h516909a_1
        - bioconductor-genomeinfodb 1.20.0 r36_1
        - bioconductor-genomeinfodbdata 1.2.1 r36_1
        - bioconductor-genomicranges 1.36.0 r36h516909a_1
        - bioconductor-impute 1.58.0 r36h6e990d7_1
        - bioconductor-iranges 2.18.1 r36h516909a_0
        - bioconductor-limma 3.40.2 r36h516909a_0
        - bioconductor-msnbase 2.10.1 r36he1b5a44_0
        - bioconductor-mzid 1.22.0 r36_1
        - bioconductor-mzr 2.18.0 r36he1b5a44_1
        - bioconductor-pcamethods 1.76.0 r36he1b5a44_1
        - bioconductor-preprocesscore 1.46.0 r36h516909a_1
        - bioconductor-protgenerics 1.16.0 r36_1
        - bioconductor-rhdf5lib 1.6.0 r36h516909a_1
        - bioconductor-s4vectors 0.22.0 r36h516909a_1
        - bioconductor-summarizedexperiment 1.14.0 r36_1
        - bioconductor-vsn 3.52.0 r36h516909a_1
        - bioconductor-xvector 0.24.0 r36h516909a_1
        - bioconductor-zlibbioc 1.30.0 r36h516909a_1
        - bwidget 1.9.11 0
        - bzip2 1.0.8 h516909a_0
        - ca-certificates 2019.6.16 hecc5488_0
        - cairo 1.16.0 hfb77d84_1002
        - curl 7.65.3 hf8cf82a_0
        - fontconfig 2.13.1 h86ecdb6_1001
        - freetype 2.10.0 he983fc9_0
        - fribidi 1.0.5 h516909a_1002
        - gcc_impl_linux-64 7.3.0 habb00fd_1
        - gcc_linux-64 7.3.0 h553295d_7
        - gettext 0.19.8.1 hc5be6a0_1002
        - gfortran_impl_linux-64 7.3.0 hdf63c60_1
        - gfortran_linux-64 7.3.0 h553295d_7
        - glib 2.58.3 h6f030ca_1002
        - graphite2 1.3.13 hf484d3e_1000
        - gsl 2.5 h294904e_0
        - gxx_impl_linux-64 7.3.0 hdf63c60_1
        - gxx_linux-64 7.3.0 h553295d_7
        - harfbuzz 2.4.0 h9f30f68_2
        - hdf4 4.2.13 h9a582f1_1002
        - hdf5 1.10.5 nompi_h3c11f04_1100
        - icu 64.2 he1b5a44_0
        - jpeg 9c h14c3975_1001
        - krb5 1.16.3 h05b26f9_1001
        - libblas 3.8.0 11_openblas
        - libcblas 3.8.0 11_openblas
        - libcurl 7.65.3 hda55be3_0
        - libedit 3.1.20170329 hf8c457e_1001
        - libffi 3.2.1 he1b5a44_1006
        - libgcc-ng 9.1.0 hdf63c60_0
        - libgfortran-ng 7.3.0 hdf63c60_0
        - libiconv 1.15 h516909a_1005
        - liblapack 3.8.0 11_openblas
        - libnetcdf 4.6.2 h056eaf5_1002
        - libopenblas 0.3.6 h6e990d7_6
        - libpng 1.6.37 hed695b0_0
        - libssh2 1.8.2 h22169c7_2
        - libstdcxx-ng 9.1.0 hdf63c60_0
        - libtiff 4.0.10 h57b8799_1003
        - libuuid 2.32.1 h14c3975_1000
        - libxcb 1.13 h14c3975_1002
        - libxml2 2.9.9 hee79883_2
        - lz4-c 1.8.3 he1b5a44_1001
        - make 4.2.1 h14c3975_2004
        - ncurses 6.1 hf484d3e_1002
        - openssl 1.1.1c h516909a_0
        - pandoc 2.7.3 0
        - pango 1.42.4 he7ab937_0
        - pcre 8.41 hf484d3e_1003
        - pixman 0.38.0 h516909a_1003
        - pthread-stubs 0.4 h14c3975_1001
        - r-assertthat 0.2.1 r36h6115d3f_1
        - r-backports 1.1.4 r36hcdcec82_1
        - r-base 3.6.1 h6e652e1_3
        - r-base64enc 0.1_3 r36hcdcec82_1003
        - r-bh 1.69.0_1 r36h6115d3f_1
        - r-biocmanager 1.30.4 r36h6115d3f_1001
        - r-bitops 1.0_6 r36hcdcec82_1003
        - r-circlize 0.4.6 r36_1
        - r-cli 1.1.0 r36h6115d3f_1
        - r-clipr 0.7.0 r36h6115d3f_0
        - r-clue 0.3_57 r36h516909a_1
        - r-cluster 2.1.0 r36h9bbef5b_1
        - r-codetools 0.2_16 r36h6115d3f_1001
        - r-colorspace 1.4_1 r36hcdcec82_1
        - r-crayon 1.3.4 r36h6115d3f_1002
        - r-crosstalk 1.0.0 r36h6115d3f_1002
        - r-digest 0.6.20 r36h0357c0b_1
        - r-doparallel 1.0.15 r36h6115d3f_0
        - r-dplyr 0.8.3 r36h0357c0b_1
        - r-dt 0.7 r36h6115d3f_1
        - r-ellipsis 0.2.0.1 r36hcdcec82_1
        - r-evaluate 0.14 r36h6115d3f_1
        - r-fansi 0.4.0 r36hcdcec82_1001
        - r-fdrtool 1.2.15 r36hcdcec82_1002
        - r-foreach 1.4.7 r36h6115d3f_0
        - r-formatr 1.7 r36h6115d3f_1
        - r-futile.logger 1.4.3 r36h6115d3f_1002
        - r-futile.options 1.0.1 r36h6115d3f_1001
        - r-getoptlong 0.1.7 r36_1002
        - r-ggplot2 3.2.0 r36h6115d3f_1
        - r-ggrepel 0.8.1 r36h0357c0b_1
        - r-globaloptions 0.1.0 r36_2002
        - r-glue 1.3.1 r36hcdcec82_1
        - r-gmm 1.6_2 r36h6115d3f_1001
        - r-gridextra 2.3 r36h6115d3f_1002
        - r-gtable 0.3.0 r36h6115d3f_2
        - r-highr 0.8 r36h6115d3f_1
        - r-hms 0.5.0 r36h6115d3f_1
        - r-htmltools 0.3.6 r36he1b5a44_1003
        - r-htmlwidgets 1.3 r36h6115d3f_1001
        - r-httpuv 1.5.1 r36h0357c0b_1
        - r-imputelcmd 2.0 r36h6115d3f_1
        - r-iterators 1.0.12 r36h6115d3f_0
        - r-jsonlite 1.6 r36hcdcec82_1001
        - r-knitr 1.23 r36h6115d3f_1
        - r-labeling 0.3 r36h6115d3f_1002
        - r-lambda.r 1.2.3 r36h6115d3f_1001
        - r-later 0.8.0 r36h0357c0b_1
        - r-lattice 0.20_38 r36hcdcec82_1002
        - r-lazyeval 0.2.2 r36hcdcec82_1
        - r-magrittr 1.5 r36h6115d3f_1002
        - r-maldiquant 1.19.3 r36h516909a_1
        - r-markdown 1.0 r36hcdcec82_1
        - r-mass 7.3_51.4 r36hcdcec82_1
        - r-matrix 1.2_17 r36hcdcec82_1
        - r-matrixstats 0.54.0 r36hcdcec82_1001
        - r-mgcv 1.8_28 r36hcdcec82_1
        - r-mime 0.7 r36hcdcec82_1
        - r-munsell 0.5.0 r36h6115d3f_1002
        - r-mvtnorm 1.0_11 r36h9bbef5b_1
        - r-ncdf4 1.16.1 r36h9123da2_2
        - r-nlme 3.1_140 r36h9bbef5b_1
        - r-norm 1.0_9.5 r36h9bbef5b_1001
        - r-pillar 1.4.2 r36h6115d3f_2
        - r-pkgconfig 2.0.2 r36h6115d3f_1002
        - r-plogr 0.2.0 r36h6115d3f_1002
        - r-plyr 1.8.4 r36h0357c0b_1003
        - r-png 0.1_7 r36hcdcec82_1003
        - r-promises 1.0.1 r36h0357c0b_1001
        - r-purrr 0.3.2 r36hcdcec82_1
        - r-r6 2.4.0 r36h6115d3f_2
        - r-rcolorbrewer 1.1_2 r36h6115d3f_1002
        - r-rcpp 1.0.2 r36h0357c0b_0
        - r-rcurl 1.95_4.12 r36hcdcec82_1
        - r-readr 1.3.1 r36h0357c0b_1001
        - r-reshape2 1.4.3 r36h0357c0b_1004
        - r-rjson 0.2.20 r36h0357c0b_1001
        - r-rlang 0.4.0 r36hcdcec82_1
        - r-rmarkdown 1.14 r36h6115d3f_1
        - r-sandwich 2.5_1 r36h6115d3f_1
        - r-scales 1.0.0 r36h0357c0b_1002
        - r-shape 1.4.4 r36_1002
        - r-shiny 1.3.2 r36h6115d3f_1
        - r-shinydashboard 0.7.1 r36h6115d3f_1001
        - r-snow 0.4_3 r36h6115d3f_1001
        - r-sourcetools 0.1.7 r36he1b5a44_1001
        - r-stringi 1.4.3 r36h0e574ca_3
        - r-stringr 1.4.0 r36h6115d3f_1
        - r-tibble 2.1.3 r36hcdcec82_1
        - r-tidyr 0.8.3 r36h0357c0b_1
        - r-tidyselect 0.2.5 r36h0357c0b_1001
        - r-tinytex 0.14 r36h6115d3f_1
        - r-tmvtnorm 1.4_10 r36h9bbef5b_1001
        - r-utf8 1.1.4 r36hcdcec82_1001
        - r-vctrs 0.2.0 r36hcdcec82_1
        - r-viridislite 0.3.0 r36h6115d3f_1002
        - r-withr 2.1.2 r36h6115d3f_1001
        - r-xfun 0.8 r36h6115d3f_1
        - r-xml 3.98_1.20 r36hcdcec82_1
        - r-xtable 1.8_4 r36h6115d3f_2
        - r-yaml 2.2.0 r36hcdcec82_1002
        - r-zeallot 0.1.0 r36h6115d3f_1001
        - r-zoo 1.8_6 r36hcdcec82_1
        - readline 8.0 hf8c457e_0
        - sed 4.7 h1bed415_1000
        - tk 8.6.9 hed695b0_1002
        - tktable 2.10 h555a92e_1
        - xorg-kbproto 1.0.7 h14c3975_1002
        - xorg-libice 1.0.10 h516909a_0
        - xorg-libsm 1.2.3 h84519dc_1000
        - xorg-libx11 1.6.8 h516909a_0
        - xorg-libxau 1.0.9 h14c3975_0
        - xorg-libxdmcp 1.1.3 h516909a_0
        - xorg-libxext 1.3.4 h516909a_0
        - xorg-libxrender 0.9.10 h516909a_1002
        - xorg-renderproto 0.11.1 h14c3975_1002
        - xorg-xextproto 7.3.0 h14c3975_1002
        - xorg-xproto 7.0.31 h14c3975_1007
        - xz 5.2.4 h14c3975_1001
        - zlib 1.2.11 h516909a_1005
        - zstd 1.4.0 h3b9ef0a_0
    run:
        - bioconductor-complexheatmap >=2.0.0,<2.1.0
        - bioconductor-limma >=3.40.0,<3.41.0
        - bioconductor-msnbase >=2.10.0,<2.11.0
        - bioconductor-summarizedexperiment >=1.14.0,<1.15.0
        - bioconductor-vsn >=3.52.0,<3.53.0
        - r-assertthat
        - r-base >=3.6,<3.7.0a0
        - r-circlize
        - r-cluster
        - r-dplyr
        - r-dt
        - r-fdrtool
        - r-ggplot2
        - r-ggrepel
        - r-gridextra
        - r-imputelcmd
        - r-purrr
        - r-rcolorbrewer
        - r-readr
        - r-rmarkdown
        - r-shiny
        - r-shinydashboard
        - r-tibble
        - r-tidyr
test:
    commands:
        - $R -e "library('DEP')"
about:
    home: https://bioconductor.org/packages/3.9/bioc/html/DEP.html
    license: Artistic-2.0
    summary: This package provides an integrated analysis workflow for robust and
        reproducible analysis of mass spectrometry proteomics data for differential
        protein expression or differential enrichment. It requires tabular input (e.g.
        txt files) as generated by quantitative analysis softwares of raw mass spectrometry
        data, such as MaxQuant or IsobarQuant. Functions are provided for data preparation,
        filtering, variance normalization and imputation of missing values, as well
        as statistical testing of differentially enriched / expressed proteins. It
        also includes tools to check intermediate steps in the workflow, such as normalization
        and missing values imputation. Finally, visualization tools are provided to
        explore the results, including heatmap, volcano plot and barplot representations.
        For scientists with limited experience in R, the package also contains wrapper
        functions that entail the complete analysis workflow and generate a report.
        Even easier to use are the interactive Shiny apps that are provided by the
        package.
extra:
    copy_test_source_files: true
    final: true
