# This file created by conda-build 24.7.1
# meta.yaml template originally from:
# /opt/recipe, last modified Tue Dec 31 21:44:14 2024
# ------------------------------------------------

package:
  name: bioconductor-cleanuprnaseq
  version: 1.0.0
source:
  md5: 3fff7d3325a4839106824d215c6f1876
  url:
    - https://bioarchive.galaxyproject.org/CleanUpRNAseq_1.0.0.tar.gz
    - https://bioconductor.org/packages/3.20/bioc/src/contrib/Archive/CleanUpRNAseq/CleanUpRNAseq_1.0.0.tar.gz
    - https://bioconductor.org/packages/3.20/bioc/src/contrib/CleanUpRNAseq_1.0.0.tar.gz
    - https://depot.galaxyproject.org/software/bioconductor-cleanuprnaseq/bioconductor-cleanuprnaseq_1.0.0_src_all.tar.gz
build:
  noarch: generic
  number: '0'
  rpaths:
    - lib/
    - lib/R/lib/
  run_exports: bioconductor-cleanuprnaseq >=1.0.0,<1.1.0a0
  string: r44hdfd78af_0
requirements:
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - _r-mutex 1.0.1 anacondar_1
    - argcomplete 3.5.2 pyhd8ed1ab_0
    - binutils_impl_linux-64 2.43 h4bf12b8_2
    - bioconductor-annotate 1.84.0 r44hdfd78af_0
    - bioconductor-annotationdbi 1.68.0 r44hdfd78af_0
    - bioconductor-annotationfilter 1.30.0 r44hdfd78af_0
    - bioconductor-biobase 2.66.0 r44h3df3fcb_0
    - bioconductor-biocgenerics 0.52.0 r44hdfd78af_0
    - bioconductor-biocio 1.16.0 r44hdfd78af_0
    - bioconductor-biocparallel 1.40.0 r44he5774e6_0
    - bioconductor-biostrings 2.74.0 r44h3df3fcb_0
    - bioconductor-bsgenome 1.74.0 r44hdfd78af_0
    - bioconductor-data-packages 20241220 hdfd78af_0
    - bioconductor-delayedarray 0.32.0 r44h3df3fcb_0
    - bioconductor-deseq2 1.46.0 r44he5774e6_0
    - bioconductor-edger 4.4.0 r44h3df3fcb_0
    - bioconductor-ensembldb 2.30.0 r44hdfd78af_0
    - bioconductor-genefilter 1.88.0 r44h81e381d_0
    - bioconductor-genomeinfodb 1.42.0 r44hdfd78af_0
    - bioconductor-genomeinfodbdata 1.2.13 r44hdfd78af_0
    - bioconductor-genomicalignments 1.42.0 r44h3df3fcb_0
    - bioconductor-genomicfeatures 1.58.0 r44hdfd78af_0
    - bioconductor-genomicranges 1.58.0 r44h3df3fcb_0
    - bioconductor-iranges 2.40.0 r44h3df3fcb_0
    - bioconductor-keggrest 1.46.0 r44hdfd78af_0
    - bioconductor-limma 3.62.0 r44h3df3fcb_0
    - bioconductor-matrixgenerics 1.18.0 r44hdfd78af_0
    - bioconductor-protgenerics 1.38.0 r44hdfd78af_1
    - bioconductor-qsmooth 1.22.0 r44hdfd78af_0
    - bioconductor-rhtslib 3.2.0 r44h15a9599_1
    - bioconductor-rsamtools 2.22.0 r44h77050f0_0
    - bioconductor-rsubread 2.20.0 r44h15a9599_0
    - bioconductor-rtracklayer 1.66.0 r44h15a9599_0
    - bioconductor-s4arrays 1.6.0 r44h3df3fcb_0
    - bioconductor-s4vectors 0.44.0 r44h3df3fcb_0
    - bioconductor-sparsearray 1.6.0 r44h3df3fcb_0
    - bioconductor-summarizedexperiment 1.36.0 r44hdfd78af_0
    - bioconductor-sva 3.54.0 r44h3df3fcb_0
    - bioconductor-tximport 1.34.0 r44hdfd78af_0
    - bioconductor-ucsc.utils 1.2.0 r44hdfd78af_0
    - bioconductor-xvector 0.46.0 r44h15a9599_0
    - bioconductor-zlibbioc 1.52.0 r44h3df3fcb_0
    - bwidget 1.10.1 ha770c72_0
    - bzip2 1.0.8 h4bc722e_7
    - c-ares 1.34.4 hb9d3cd8_0
    - ca-certificates 2024.12.14 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 10.1.0 h0b3b770_0
    - icu 75.1 he02047a_0
    - jq 1.7.1 hd590300_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 26_linux64_openblas
    - libcblas 3.9.0 26_linux64_openblas
    - libcurl 8.11.1 h332b0f4_0
    - libdeflate 1.23 h4ddbbb0_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 26_linux64_openblas
    - liblzma 5.6.3 hb9d3cd8_1
    - libmpdec 4.0.0 h4bc722e_0
    - 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
    - libsqlite 3.47.2 hee588c1_0
    - 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 hd9ff511_3
    - libuuid 2.38.1 h0b41bf4_0
    - libwebp-base 1.5.0 h851e524_0
    - libxcb 1.17.0 h8a09558_0
    - libxml2 2.13.5 h8d12d68_1
    - libzlib 1.3.1 hb9d3cd8_2
    - make 4.4.1 hb9d3cd8_2
    - ncurses 6.5 he02047a_1
    - oniguruma 6.9.9 hd590300_0
    - openssl 3.4.0 hb9d3cd8_0
    - pandoc 3.6.1 ha770c72_0
    - pango 1.54.0 h861ebed_4
    - pcre2 10.44 hba22ea6_2
    - pip 24.3.1 pyh145f28c_2
    - pixman 0.44.2 h29eaf8c_0
    - pthread-stubs 0.4 hb9d3cd8_1002
    - python 3.13.1 ha99a958_102_cp313
    - python_abi 3.13 5_cp313
    - pyyaml 6.0.2 py313h536fd9c_1
    - r-abind 1.4_5 r44hc72bb7e_1006
    - r-askpass 1.2.1 r44h2b5f3a1_0
    - r-backports 1.5.0 r44hb1dbf0f_1
    - r-base 4.4.2 hc737e89_2
    - r-base64enc 0.1_3 r44hb1dbf0f_1007
    - r-bh 1.87.0_1 r44hc72bb7e_0
    - r-bit 4.5.0.1 r44h2b5f3a1_0
    - r-bit64 4.5.2 r44h2b5f3a1_0
    - r-bitops 1.0_9 r44h2b5f3a1_0
    - r-blob 1.2.4 r44hc72bb7e_2
    - r-bslib 0.8.0 r44hc72bb7e_0
    - r-cachem 1.1.0 r44hb1dbf0f_1
    - r-checkmate 2.3.2 r44hdb488b9_0
    - r-cli 3.6.3 r44h0d4f4ea_1
    - r-cluster 2.1.8 r44hb67ce94_0
    - r-codetools 0.2_20 r44hc72bb7e_1
    - r-colorspace 2.1_1 r44hdb488b9_0
    - r-cpp11 0.5.1 r44hc72bb7e_0
    - r-crayon 1.5.3 r44hc72bb7e_1
    - r-curl 6.0.1 r44h2700575_0
    - r-data.table 1.15.4 r44h5f06984_1
    - r-dbi 1.2.3 r44hc72bb7e_1
    - r-deldir 2.0_4 r44hbcb9c34_1
    - r-digest 0.6.37 r44h0d4f4ea_0
    - r-ellipsis 0.3.2 r44hb1dbf0f_3
    - r-evaluate 1.0.1 r44hc72bb7e_0
    - r-fansi 1.0.6 r44hb1dbf0f_1
    - r-farver 2.1.2 r44ha18555a_1
    - r-fastmap 1.2.0 r44ha18555a_1
    - r-fontawesome 0.5.3 r44hc72bb7e_0
    - r-foreign 0.8_87 r44hb1dbf0f_1
    - r-formatr 1.14 r44hc72bb7e_2
    - r-formula 1.2_5 r44hc72bb7e_2
    - r-fs 1.6.5 r44h93ab643_0
    - r-futile.logger 1.4.3 r44hc72bb7e_1006
    - r-futile.options 1.0.1 r44hc72bb7e_1005
    - r-ggplot2 3.5.1 r44hc72bb7e_1
    - r-ggrepel 0.9.6 r44h93ab643_0
    - r-glue 1.8.0 r44h2b5f3a1_0
    - r-gridextra 2.3 r44hc72bb7e_1006
    - r-gtable 0.3.6 r44hc72bb7e_0
    - r-highr 0.11 r44hc72bb7e_1
    - r-hmisc 5.2_1 r44hb67ce94_0
    - r-htmltable 2.4.3 r44hc72bb7e_0
    - r-htmltools 0.5.8.1 r44ha18555a_1
    - r-htmlwidgets 1.6.4 r44h785f33e_3
    - r-httr 1.4.7 r44hc72bb7e_1
    - r-interp 1.1_6 r44ha936806_1
    - r-isoband 0.2.7 r44ha18555a_3
    - r-jpeg 0.1_10 r44had62be2_6
    - r-jquerylib 0.1.4 r44hc72bb7e_3
    - r-jsonlite 1.8.9 r44h2b5f3a1_0
    - r-kernsmooth 2.23_24 r44hc2011d3_1
    - r-knitr 1.49 r44hc72bb7e_0
    - r-labeling 0.4.3 r44hc72bb7e_1
    - r-lambda.r 1.2.4 r44hc72bb7e_4
    - r-lattice 0.22_6 r44hb1dbf0f_1
    - r-latticeextra 0.6_30 r44hc72bb7e_3
    - r-lazyeval 0.2.2 r44hb1dbf0f_5
    - r-lifecycle 1.0.4 r44hc72bb7e_1
    - r-locfit 1.5_9.10 r44h2b5f3a1_0
    - r-magrittr 2.0.3 r44hb1dbf0f_3
    - r-mass 7.3_60.0.1 r44hb1dbf0f_1
    - r-matrix 1.6_5 r44he966344_1
    - r-matrixstats 1.4.1 r44h2b5f3a1_0
    - r-memoise 2.0.1 r44hc72bb7e_3
    - r-mgcv 1.9_1 r44h0d28552_1
    - r-mime 0.12 r44hb1dbf0f_3
    - r-munsell 0.5.1 r44hc72bb7e_1
    - r-nlme 3.1_165 r44hbcb9c34_1
    - r-nnet 7.3_19 r44hb1dbf0f_2
    - r-openssl 2.2.2 r44he8289e2_0
    - r-pheatmap 1.0.12 r44hc72bb7e_5
    - r-pillar 1.10.0 r44hc72bb7e_0
    - r-pkgconfig 2.0.3 r44hc72bb7e_4
    - r-plogr 0.2.0 r44hc72bb7e_1006
    - r-plyr 1.8.9 r44ha18555a_1
    - r-png 0.1_8 r44h21f035c_2
    - r-r6 2.5.1 r44hc72bb7e_3
    - r-rappdirs 0.3.3 r44hb1dbf0f_3
    - r-rcolorbrewer 1.1_3 r44h785f33e_3
    - r-rcpp 1.0.13_1 r44h93ab643_0
    - r-rcpparmadillo 14.2.2_1 r44hb79369c_0
    - r-rcppeigen 0.3.4.0.2 r44hb79369c_0
    - r-rcurl 1.98_1.16 r44he8228da_1
    - r-reshape2 1.4.4 r44h0d4f4ea_4
    - r-restfulr 0.0.15 r44h5ef9028_5
    - r-rjson 0.2.23 r44h93ab643_0
    - r-rlang 1.1.4 r44ha18555a_1
    - r-rmarkdown 2.29 r44hc72bb7e_0
    - r-rpart 4.1.23 r44hb1dbf0f_1
    - r-rsqlite 2.3.9 r44h93ab643_0
    - r-rstudioapi 0.17.1 r44hc72bb7e_0
    - r-sass 0.4.9 r44ha18555a_1
    - r-scales 1.3.0 r44hc72bb7e_1
    - r-snow 0.4_4 r44hc72bb7e_3
    - r-statmod 1.5.0 r44ha36c22a_2
    - r-stringi 1.8.4 r44h33cde33_3
    - r-stringr 1.5.1 r44h785f33e_1
    - r-survival 3.8_3 r44h2b5f3a1_0
    - r-sys 3.4.3 r44h2b5f3a1_0
    - r-tibble 3.2.1 r44hdb488b9_3
    - r-tinytex 0.54 r44hc72bb7e_0
    - r-utf8 1.2.4 r44hb1dbf0f_1
    - r-vctrs 0.6.5 r44h0d4f4ea_1
    - r-viridis 0.6.5 r44hc72bb7e_1
    - r-viridislite 0.4.2 r44hc72bb7e_2
    - r-withr 3.0.2 r44hc72bb7e_0
    - r-xfun 0.49 r44h93ab643_0
    - r-xml 3.99_0.17 r44h5bae778_2
    - r-xtable 1.8_4 r44hc72bb7e_6
    - r-yaml 2.3.10 r44hdb488b9_0
    - readline 8.2 h8228510_1
    - sed 4.8 he412f7d_0
    - setuptools 75.6.0 pyhff2d567_1
    - sysroot_linux-64 2.17 h0157908_18
    - tk 8.6.13 noxft_h4845f30_101
    - tktable 2.10 h8bc8fbc_6
    - toml 0.10.2 pyhd8ed1ab_1
    - tomlkit 0.13.2 pyha770c72_1
    - tzdata 2024b hc8b5060_0
    - xmltodict 0.14.2 pyhd8ed1ab_1
    - xorg-libice 1.1.2 hb9d3cd8_0
    - xorg-libsm 1.2.5 he73a12e_0
    - xorg-libx11 1.8.10 h4f16b4b_1
    - xorg-libxau 1.0.12 hb9d3cd8_0
    - xorg-libxdmcp 1.1.5 hb9d3cd8_0
    - xorg-libxext 1.3.6 hb9d3cd8_0
    - xorg-libxrender 0.9.12 hb9d3cd8_0
    - xorg-libxt 1.3.1 hb9d3cd8_0
    - yaml 0.2.5 h7f98852_2
    - yq 3.4.3 pyhd8ed1ab_1
    - zstd 1.5.6 ha6fb4c9_0
  run:
    - bioconductor-annotationfilter >=1.30.0,<1.31.0
    - bioconductor-biocgenerics >=0.52.0,<0.53.0
    - bioconductor-biostrings >=2.74.0,<2.75.0
    - bioconductor-bsgenome >=1.74.0,<1.75.0
    - bioconductor-deseq2 >=1.46.0,<1.47.0
    - bioconductor-edger >=4.4.0,<4.5.0
    - bioconductor-ensembldb >=2.30.0,<2.31.0
    - bioconductor-genomeinfodb >=1.42.0,<1.43.0
    - bioconductor-genomicranges >=1.58.0,<1.59.0
    - bioconductor-limma >=3.62.0,<3.63.0
    - bioconductor-qsmooth >=1.22.0,<1.23.0
    - bioconductor-rsamtools >=2.22.0,<2.23.0
    - bioconductor-rsubread >=2.20.0,<2.21.0
    - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
    - bioconductor-tximport >=1.34.0,<1.35.0
    - r-base >=4.4,<4.5.0a0
    - r-base >=4.4,<4.5.0a0
    - r-ggplot2
    - r-ggrepel
    - r-kernsmooth
    - r-pheatmap
    - r-r6
    - r-rcolorbrewer
    - r-reshape2
test:
  commands:
    - $R -e "library('CleanUpRNAseq')"
about:
  description: RNA-seq data generated by some library preparation methods, such as
    rRNA-depletion-based method and the SMART-seq method, might be contaminated by
    genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA
    preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from
    gDNA contamination. If so, it can perform correction for gDNA contamination and
    reduce false discovery rate of differentially expressed genes.
  home: https://bioconductor.org/packages/3.20/bioc/html/CleanUpRNAseq.html
  license: GPL-3
  license_file: /opt/conda/conda-bld/bioconductor-cleanuprnaseq_1735694789431/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/share/licenses/GPL-3
  summary: Detect and Correct Genomic DNA Contamination in RNA-seq Data
extra:
  copy_test_source_files: true
  final: true
