# This file created by conda-build 3.17.8
# meta.yaml template originally from:
# /opt/recipe, last modified Fri May 10 15:31:57 2019
# ------------------------------------------------

package:
    name: bioconductor-rnadecay
    version: 1.4.0
source:
    md5: 7fe84f6a5edb236cf8dcd1a88f649155
    url:
        - https://bioarchive.galaxyproject.org/RNAdecay_1.4.0.tar.gz
        - https://bioconductor.org/packages/3.9/bioc/src/contrib/RNAdecay_1.4.0.tar.gz
        - https://depot.galaxyproject.org/software/bioconductor-rnadecay/bioconductor-rnadecay_1.4.0_src_all.tar.gz
build:
    number: '0'
    rpaths:
        - lib/
        - lib/R/lib/
    string: r351hf484d3e_0
requirements:
    build:
        - binutils_impl_linux-64 2.31.1 h6176602_1
        - binutils_linux-64 2.31.1 h6176602_7
        - gcc_impl_linux-64 7.3.0 habb00fd_1
        - gcc_linux-64 7.3.0 h553295d_7
        - gxx_impl_linux-64 7.3.0 hdf63c60_1
        - gxx_linux-64 7.3.0 h553295d_7
        - libgcc-ng 8.2.0 hdf63c60_1
        - libstdcxx-ng 8.2.0 hdf63c60_1
        - make 4.2.1 h14c3975_2004
    host:
        - _r-mutex 1.0.0 anacondar_1
        - binutils_impl_linux-64 2.31.1 h6176602_1
        - binutils_linux-64 2.31.1 h6176602_7
        - bwidget 1.9.11 1
        - bzip2 1.0.6 h14c3975_1002
        - ca-certificates 2019.3.9 hecc5488_0
        - cairo 1.16.0 ha4e643d_1000
        - curl 7.64.1 hf8cf82a_0
        - fontconfig 2.13.1 he4413a7_1000
        - freetype 2.10.0 he983fc9_0
        - 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 hf63aee3_1001
        - graphite2 1.3.13 hf484d3e_1000
        - gsl 2.4 h294904e_1006
        - gxx_impl_linux-64 7.3.0 hdf63c60_1
        - gxx_linux-64 7.3.0 h553295d_7
        - harfbuzz 2.4.0 h37c48d4_0
        - icu 58.2 hf484d3e_1000
        - jpeg 9c h14c3975_1001
        - krb5 1.16.3 h05b26f9_1001
        - libblas 3.8.0 8_openblas
        - libcblas 3.8.0 8_openblas
        - libcurl 7.64.1 hda55be3_0
        - libedit 3.1.20170329 hf8c457e_1001
        - libffi 3.2.1 he1b5a44_1006
        - libgcc-ng 8.2.0 hdf63c60_1
        - libgfortran-ng 7.3.0 hdf63c60_0
        - libiconv 1.15 h516909a_1005
        - libpng 1.6.37 hed695b0_0
        - libssh2 1.8.2 h22169c7_2
        - libstdcxx-ng 8.2.0 hdf63c60_1
        - libtiff 4.0.10 h648cc4a_1001
        - libuuid 2.32.1 h14c3975_1000
        - libxcb 1.13 h14c3975_1002
        - libxml2 2.9.9 h13577e0_0
        - make 4.2.1 h14c3975_2004
        - ncurses 6.1 hf484d3e_1002
        - openblas 0.3.6 h6e990d7_1
        - openssl 1.1.1b h14c3975_1
        - pango 1.40.14 h4ea9474_1004
        - pcre 8.41 hf484d3e_1003
        - pixman 0.34.0 h14c3975_1003
        - pthread-stubs 0.4 h14c3975_1001
        - r-assertthat 0.2.1 r351h6115d3f_0
        - r-base 3.5.1 h271c98b_1006
        - r-bitops 1.0_6 r351h96ca727_1002
        - r-catools 1.17.1.2 r351h29659fb_0
        - r-cli 1.1.0 r351h6115d3f_0
        - r-colorspace 1.4_1 r351hcdcec82_0
        - r-crayon 1.3.4 r351h6115d3f_1001
        - r-digest 0.6.18 r351h96ca727_1000
        - r-fansi 0.4.0 r351h96ca727_1000
        - r-gdata 2.18.0 r351h6115d3f_1001
        - r-ggplot2 3.1.1 r351h6115d3f_0
        - r-glue 1.3.1 r351hcdcec82_0
        - r-gplots 3.0.1.1 r351h6115d3f_0
        - r-gtable 0.3.0 r351h6115d3f_0
        - r-gtools 3.8.1 r351h96ca727_1002
        - r-kernsmooth 2.23_15 r351ha65eedd_1002
        - r-labeling 0.3 r351h6115d3f_1001
        - r-lattice 0.20_38 r351h96ca727_1000
        - r-lazyeval 0.2.2 r351hcdcec82_0
        - r-magrittr 1.5 r351h6115d3f_1001
        - r-mass 7.3_51.4 r351hcdcec82_0
        - r-matrix 1.2_17 r351hcdcec82_0
        - r-mgcv 1.8_28 r351hcdcec82_0
        - r-munsell 0.5.0 r351h6115d3f_1001
        - r-nlme 3.1_139 r351h9bbef5b_0
        - r-nloptr 1.2.1 r351h29659fb_0
        - r-pillar 1.3.1 r351h6115d3f_1000
        - r-pkgconfig 2.0.2 r351h6115d3f_1001
        - r-plyr 1.8.4 r351h29659fb_1002
        - r-r6 2.4.0 r351h6115d3f_0
        - r-rcolorbrewer 1.1_2 r351h6115d3f_1001
        - r-rcpp 1.0.1 r351h0357c0b_0
        - r-rcppeigen 0.3.3.5.0 r351h29659fb_0
        - r-reshape2 1.4.3 r351h29659fb_1003
        - r-rlang 0.3.4 r351hcdcec82_0
        - r-scales 1.0.0 r351h29659fb_1001
        - r-stringi 1.4.3 r351h0357c0b_0
        - r-stringr 1.4.0 r351h6115d3f_0
        - r-tibble 2.1.1 r351hcdcec82_0
        - r-tmb 1.7.14 r351h29659fb_1002
        - r-utf8 1.1.4 r351h96ca727_1000
        - r-viridislite 0.3.0 r351h6115d3f_1001
        - r-withr 2.1.2 r351h6115d3f_1000
        - readline 7.0 hf8c457e_1001
        - tk 8.6.9 h84994c4_1001
        - tktable 2.10 h14c3975_0
        - xorg-kbproto 1.0.7 h14c3975_1002
        - xorg-libice 1.0.9 h516909a_1004
        - xorg-libsm 1.2.3 h84519dc_1000
        - xorg-libx11 1.6.7 h14c3975_1000
        - 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 h14c3975_1004
    run:
        - libgcc-ng >=7.3.0
        - libstdcxx-ng >=7.3.0
        - r-base >=3.5.1,<3.5.2.0a0
        - r-ggplot2
        - r-gplots
        - r-nloptr
        - r-tmb
test:
    commands:
        - $R -e "library('RNAdecay')"
about:
    home: https://bioconductor.org/packages/3.9/bioc/html/RNAdecay.html
    license: GPL-2
    summary: 'RNA degradation is monitored through measurement of RNA abundance after
        inhibiting RNA synthesis. This package has functions and example scripts to
        facilitate (1) data normalization, (2) data modeling using constant decay
        rate or time-dependent decay rate models, (3) the evaluation of treatment
        or genotype effects, and (4) plotting of the data and models. Data Normalization:
        functions and scripts make easy the normalization to the initial (T0) RNA
        abundance, as well as a method to correct for artificial inflation of Reads
        per Million (RPM) abundance in global assessments as the total size of the
        RNA pool decreases. Modeling: Normalized data is then modeled using maximum
        likelihood to fit parameters. For making treatment or genotype comparisons
        (up to four), the modeling step models all possible treatment effects on each
        gene by repeating the modeling with constraints on the model parameters (i.e.,
        the decay rate of treatments A and B are modeled once with them being equal
        and again allowing them to both vary independently). Model Selection: The
        AICc value is calculated for each model, and the model with the lowest AICc
        is chosen. Modeling results of selected models are then compiled into a single
        data frame. Graphical Plotting: a function is provided to easily visualize
        the data and the selected model using ggplot2 package functions.'
extra:
    copy_test_source_files: true
    final: true
