# This file created by conda-build 24.7.1
# meta.yaml template originally from:
# /opt/recipe, last modified Sat Dec 14 13:52:35 2024
# ------------------------------------------------

package:
  name: bioconductor-gigsea
  version: 1.24.0
source:
  md5: 6be6e775cb39122d45921cfdb767abe3
  url:
    - https://bioarchive.galaxyproject.org/GIGSEA_1.24.0.tar.gz
    - https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/GIGSEA/GIGSEA_1.24.0.tar.gz
    - https://bioconductor.org/packages/3.20/bioc/src/contrib/GIGSEA_1.24.0.tar.gz
    - https://depot.galaxyproject.org/software/bioconductor-gigsea/bioconductor-gigsea_1.24.0_src_all.tar.gz
build:
  noarch: generic
  number: '0'
  rpaths:
    - lib/
    - lib/R/lib/
  run_exports: bioconductor-gigsea >=1.24.0,<1.25.0a0
  string: r44hdfd78af_0
requirements:
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - _r-mutex 1.0.1 anacondar_1
    - binutils_impl_linux-64 2.43 h4bf12b8_2
    - bwidget 1.10.1 ha770c72_0
    - bzip2 1.0.8 h4bc722e_7
    - c-ares 1.34.3 hb9d3cd8_1
    - ca-certificates 2024.8.30 hbcca054_0
    - cairo 1.18.2 h3394656_1
    - curl 8.11.1 h332b0f4_0
    - font-ttf-dejavu-sans-mono 2.37 hab24e00_0
    - font-ttf-inconsolata 3.000 h77eed37_0
    - font-ttf-source-code-pro 2.038 h77eed37_0
    - font-ttf-ubuntu 0.83 h77eed37_3
    - fontconfig 2.15.0 h7e30c49_1
    - fonts-conda-ecosystem 1 0
    - fonts-conda-forge 1 0
    - freetype 2.12.1 h267a509_2
    - fribidi 1.0.10 h36c2ea0_0
    - gcc_impl_linux-64 14.2.0 h6b349bd_1
    - gfortran_impl_linux-64 14.2.0 hc73f493_1
    - graphite2 1.3.13 h59595ed_1003
    - gsl 2.7 he838d99_0
    - gxx_impl_linux-64 14.2.0 h2c03514_1
    - harfbuzz 9.0.0 hda332d3_1
    - icu 75.1 he02047a_0
    - kernel-headers_linux-64 3.10.0 he073ed8_18
    - keyutils 1.6.1 h166bdaf_0
    - krb5 1.21.3 h659f571_0
    - ld_impl_linux-64 2.43 h712a8e2_2
    - lerc 4.0.0 h27087fc_0
    - libblas 3.9.0 25_linux64_openblas
    - libcblas 3.9.0 25_linux64_openblas
    - libcurl 8.11.1 h332b0f4_0
    - libdeflate 1.22 hb9d3cd8_0
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 hd590300_2
    - libexpat 2.6.4 h5888daf_0
    - libffi 3.4.2 h7f98852_5
    - libgcc 14.2.0 h77fa898_1
    - libgcc-devel_linux-64 14.2.0 h41c2201_101
    - libgcc-ng 14.2.0 h69a702a_1
    - libgfortran 14.2.0 h69a702a_1
    - libgfortran-ng 14.2.0 h69a702a_1
    - libgfortran5 14.2.0 hd5240d6_1
    - libglib 2.82.2 h2ff4ddf_0
    - libgomp 14.2.0 h77fa898_1
    - libiconv 1.17 hd590300_2
    - libjpeg-turbo 3.0.0 hd590300_1
    - liblapack 3.9.0 25_linux64_openblas
    - liblzma 5.6.3 hb9d3cd8_1
    - liblzma-devel 5.6.3 hb9d3cd8_1
    - libnghttp2 1.64.0 h161d5f1_0
    - libopenblas 0.3.28 pthreads_h94d23a6_1
    - libpng 1.6.44 hadc24fc_0
    - libsanitizer 14.2.0 h2a3dede_1
    - libssh2 1.11.1 hf672d98_0
    - libstdcxx 14.2.0 hc0a3c3a_1
    - libstdcxx-devel_linux-64 14.2.0 h41c2201_101
    - libstdcxx-ng 14.2.0 h4852527_1
    - libtiff 4.7.0 hc4654cb_2
    - libuuid 2.38.1 h0b41bf4_0
    - libwebp-base 1.4.0 hd590300_0
    - libxcb 1.17.0 h8a09558_0
    - libzlib 1.3.1 hb9d3cd8_2
    - make 4.4.1 hb9d3cd8_2
    - ncurses 6.5 he02047a_1
    - openssl 3.4.0 hb9d3cd8_0
    - pango 1.54.0 h3a902e7_3
    - pcre2 10.44 hba22ea6_2
    - pixman 0.44.2 h29eaf8c_0
    - pthread-stubs 0.4 hb9d3cd8_1002
    - r-base 4.4.2 h64c9cd0_0
    - r-lattice 0.22_6 r44hb1dbf0f_1
    - r-locfdr 1.1_8 r44hc72bb7e_1006
    - r-mass 7.3_60.0.1 r44hb1dbf0f_1
    - r-matrix 1.6_5 r44he966344_1
    - readline 8.2 h8228510_1
    - sed 4.8 he412f7d_0
    - sysroot_linux-64 2.17 h4a8ded7_18
    - tk 8.6.13 noxft_h4845f30_101
    - tktable 2.10 h8bc8fbc_6
    - tzdata 2024b hc8b5060_0
    - xorg-libice 1.1.1 hb9d3cd8_1
    - xorg-libsm 1.2.4 he73a12e_1
    - xorg-libx11 1.8.10 h4f16b4b_1
    - xorg-libxau 1.0.11 hb9d3cd8_1
    - xorg-libxdmcp 1.1.5 hb9d3cd8_0
    - xorg-libxext 1.3.6 hb9d3cd8_0
    - xorg-libxrender 0.9.11 hb9d3cd8_2
    - xorg-libxt 1.3.1 hb9d3cd8_0
    - xz 5.6.3 hbcc6ac9_1
    - xz-gpl-tools 5.6.3 hbcc6ac9_1
    - xz-tools 5.6.3 hb9d3cd8_1
    - zstd 1.5.6 ha6fb4c9_0
  run:
    - r-base >=4.4,<4.5.0a0
    - r-base >=4.4,<4.5.0a0
    - r-locfdr
    - r-mass
    - r-matrix
test:
  commands:
    - $R -e "library('GIGSEA')"
about:
  description: We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA),
    a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene
    expression to interrogate gene set enrichment for the trait-associated SNPs. By
    incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately
    addresses such challenges for SNP enrichment as gene size, gene boundary, SNP
    distal regulation, and multiple-marker regulation. The weighted linear regression
    model, taking as weights both imputation accuracy and model completeness, was
    used to perform the enrichment test, properly adjusting the bias due to redundancy
    in different gene sets. The permutation test, furthermore, is used to evaluate
    the significance of enrichment, whose efficiency can be largely elevated by expressing
    the computational intensive part in terms of large matrix operation. We have shown
    the appropriate type I error rates for GIGSEA (<5%), and the preliminary results
    also demonstrate its good performance to uncover the real signal.
  home: https://bioconductor.org/packages/3.20/bioc/html/GIGSEA.html
  license: LGPL-3
  license_file: /opt/conda/conda-bld/bioconductor-gigsea_1734197954591/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/lib/R/share/licenses/LGPL-3
  summary: Genotype Imputed Gene Set Enrichment Analysis
extra:
  copy_test_source_files: true
  final: true
