# This file created by conda-build 3.24.0
# meta.yaml template originally from:
# /opt/recipe, last modified Wed Jul 19 10:46:14 2023
# ------------------------------------------------

package:
  name: bioconductor-spotlight
  version: 1.4.1
source:
  md5: e3cf368e27ab8dba4f20ca904271c4ea
  url:
    - https://bioarchive.galaxyproject.org/SPOTlight_1.4.1.tar.gz
    - https://bioconductor.org/packages/3.17/bioc/src/contrib/Archive/SPOTlight/SPOTlight_1.4.1.tar.gz
    - https://bioconductor.org/packages/3.17/bioc/src/contrib/SPOTlight_1.4.1.tar.gz
    - https://depot.galaxyproject.org/software/bioconductor-spotlight/bioconductor-spotlight_1.4.1_src_all.tar.gz
build:
  noarch: generic
  number: '0'
  rpaths:
    - lib/
    - lib/R/lib/
  string: r43hdfd78af_0
requirements:
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - _r-mutex 1.0.1 anacondar_1
    - argcomplete 3.1.1 pyhd8ed1ab_0
    - binutils_impl_linux-64 2.40 hf600244_0
    - bioconductor-biobase 2.60.0 r43ha9d7317_0
    - bioconductor-biocgenerics 0.46.0 r43hdfd78af_0
    - bioconductor-data-packages 20230718 hdfd78af_1
    - bioconductor-delayedarray 0.26.6 r43ha9d7317_0
    - bioconductor-genomeinfodb 1.36.1 r43hdfd78af_0
    - bioconductor-genomeinfodbdata 1.2.10 r43hdfd78af_0
    - bioconductor-genomicranges 1.52.0 r43ha9d7317_0
    - bioconductor-iranges 2.34.1 r43ha9d7317_0
    - bioconductor-matrixgenerics 1.12.2 r43hdfd78af_0
    - bioconductor-s4arrays 1.0.4 r43ha9d7317_0
    - bioconductor-s4vectors 0.38.1 r43ha9d7317_0
    - bioconductor-singlecellexperiment 1.22.0 r43hdfd78af_0
    - bioconductor-summarizedexperiment 1.30.2 r43hdfd78af_0
    - bioconductor-xvector 0.40.0 r43ha9d7317_0
    - bioconductor-zlibbioc 1.46.0 r43ha9d7317_0
    - bwidget 1.9.14 ha770c72_1
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    - curl 8.2.0 hca28451_0
    - expat 2.5.0 hcb278e6_1
    - 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 hab24e00_0
    - fontconfig 2.14.2 h14ed4e7_0
    - fonts-conda-ecosystem 1 0
    - fonts-conda-forge 1 0
    - freetype 2.12.1 hca18f0e_1
    - fribidi 1.0.10 h36c2ea0_0
    - gcc_impl_linux-64 13.1.0 hc4be1a9_0
    - gettext 0.21.1 h27087fc_0
    - gfortran_impl_linux-64 13.1.0 hd511a9b_0
    - graphite2 1.3.13 h58526e2_1001
    - gsl 2.7 he838d99_0
    - gxx_impl_linux-64 13.1.0 hc4be1a9_0
    - harfbuzz 7.3.0 hdb3a94d_0
    - icu 72.1 hcb278e6_0
    - jq 1.6 h36c2ea0_1000
    - kernel-headers_linux-64 2.6.32 he073ed8_16
    - keyutils 1.6.1 h166bdaf_0
    - krb5 1.21.1 h659d440_0
    - ld_impl_linux-64 2.40 h41732ed_0
    - lerc 4.0.0 h27087fc_0
    - libblas 3.9.0 17_linux64_openblas
    - libcblas 3.9.0 17_linux64_openblas
    - libcurl 8.2.0 hca28451_0
    - libdeflate 1.18 h0b41bf4_0
    - libedit 3.1.20191231 he28a2e2_2
    - libev 4.33 h516909a_1
    - libexpat 2.5.0 hcb278e6_1
    - libffi 3.4.2 h7f98852_5
    - libgcc-devel_linux-64 13.1.0 he3cc6c4_0
    - libgcc-ng 13.1.0 he5830b7_0
    - libgfortran-ng 13.1.0 h69a702a_0
    - libgfortran5 13.1.0 h15d22d2_0
    - libglib 2.76.4 hebfc3b9_0
    - libgomp 13.1.0 he5830b7_0
    - libiconv 1.17 h166bdaf_0
    - libjpeg-turbo 2.1.5.1 h0b41bf4_0
    - liblapack 3.9.0 17_linux64_openblas
    - libnghttp2 1.52.0 h61bc06f_0
    - libnsl 2.0.0 h7f98852_0
    - libopenblas 0.3.23 pthreads_h80387f5_0
    - libpng 1.6.39 h753d276_0
    - libsanitizer 13.1.0 hfd8a6a1_0
    - libsqlite 3.42.0 h2797004_0
    - libssh2 1.11.0 h0841786_0
    - libstdcxx-devel_linux-64 13.1.0 he3cc6c4_0
    - libstdcxx-ng 13.1.0 hfd8a6a1_0
    - libtiff 4.5.1 h8b53f26_0
    - libuuid 2.38.1 h0b41bf4_0
    - libwebp-base 1.3.1 hd590300_0
    - libxcb 1.15 h0b41bf4_0
    - libxml2 2.11.4 h0d562d8_0
    - libzlib 1.2.13 hd590300_5
    - make 4.3 hd18ef5c_1
    - ncurses 6.4 hcb278e6_0
    - oniguruma 6.9.8 h166bdaf_0
    - openssl 3.1.1 hd590300_1
    - pango 1.50.14 heaa33ce_1
    - pcre2 10.40 hc3806b6_0
    - pip 23.2 pyhd8ed1ab_0
    - pixman 0.40.0 h36c2ea0_0
    - pthread-stubs 0.4 h36c2ea0_1001
    - python 3.11.4 hab00c5b_0_cpython
    - python_abi 3.11 3_cp311
    - pyyaml 6.0 py311hd4cff14_5
    - r-assertthat 0.2.1 r43hc72bb7e_4
    - r-backports 1.4.1 r43h57805ef_2
    - r-base 4.3.1 hb1b9b86_2
    - r-bibtex 0.5.1 r43hc72bb7e_1
    - r-bitops 1.0_7 r43h57805ef_2
    - r-cli 3.6.1 r43ha503ecb_1
    - r-cluster 2.1.4 r43h61816a4_1
    - r-codetools 0.2_19 r43hc72bb7e_1
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    - r-fansi 1.0.4 r43h57805ef_1
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    - r-foreach 1.5.2 r43hc72bb7e_2
    - r-ggplot2 3.4.2 r43hc72bb7e_1
    - r-glue 1.6.2 r43h57805ef_2
    - r-gridbase 0.4_7 r43hc72bb7e_1005
    - r-gtable 0.3.3 r43hc72bb7e_1
    - r-isoband 0.2.7 r43ha503ecb_2
    - r-iterators 1.0.14 r43hc72bb7e_2
    - r-labeling 0.4.2 r43hc72bb7e_3
    - r-lattice 0.21_8 r43h57805ef_1
    - r-lifecycle 1.0.3 r43hc72bb7e_2
    - r-magrittr 2.0.3 r43h57805ef_2
    - r-mass 7.3_60 r43h57805ef_1
    - r-matrix 1.6_0 r43h316c678_0
    - r-matrixstats 1.0.0 r43h57805ef_1
    - r-mgcv 1.9_0 r43h316c678_0
    - r-munsell 0.5.0 r43hc72bb7e_1006
    - r-nlme 3.1_162 r43h61816a4_1
    - r-nmf 0.21.0 r43ha503ecb_1006
    - r-nnls 1.4 r43h61816a4_1008
    - r-pillar 1.9.0 r43hc72bb7e_1
    - r-pkgconfig 2.0.3 r43hc72bb7e_3
    - r-pkgmaker 0.32.10 r43hc72bb7e_1
    - r-plyr 1.8.8 r43ha503ecb_1
    - r-r6 2.5.1 r43hc72bb7e_2
    - r-rcolorbrewer 1.1_3 r43h785f33e_2
    - r-rcpp 1.0.11 r43h7df8631_0
    - r-rcurl 1.98_1.12 r43hf9611b0_2
    - r-registry 0.5_1 r43hc72bb7e_4
    - r-reshape2 1.4.4 r43ha503ecb_3
    - r-rlang 1.1.1 r43ha503ecb_1
    - r-rngtools 1.5.2 r43hc72bb7e_2
    - r-scales 1.2.1 r43hc72bb7e_2
    - r-stringi 1.7.12 r43hc0c3e09_2
    - r-stringr 1.5.0 r43h785f33e_1
    - r-tibble 3.2.1 r43h57805ef_2
    - r-utf8 1.2.3 r43h57805ef_1
    - r-vctrs 0.6.3 r43ha503ecb_0
    - r-viridislite 0.4.2 r43hc72bb7e_1
    - r-withr 2.5.0 r43hc72bb7e_2
    - r-xtable 1.8_4 r43hc72bb7e_5
    - readline 8.2 h8228510_1
    - sed 4.8 he412f7d_0
    - setuptools 68.0.0 pyhd8ed1ab_0
    - sysroot_linux-64 2.12 he073ed8_16
    - tk 8.6.12 h27826a3_0
    - tktable 2.10 hb7b940f_3
    - toml 0.10.2 pyhd8ed1ab_0
    - tomlkit 0.11.8 pyha770c72_0
    - tzdata 2023c h71feb2d_0
    - wheel 0.40.0 pyhd8ed1ab_1
    - xmltodict 0.13.0 pyhd8ed1ab_0
    - xorg-kbproto 1.0.7 h7f98852_1002
    - xorg-libice 1.0.10 h7f98852_0
    - xorg-libsm 1.2.3 hd9c2040_1000
    - xorg-libx11 1.8.6 h8ee46fc_0
    - xorg-libxau 1.0.11 hd590300_0
    - xorg-libxdmcp 1.1.3 h7f98852_0
    - xorg-libxext 1.3.4 h0b41bf4_2
    - xorg-libxrender 0.9.11 hd590300_0
    - xorg-libxt 1.3.0 hd590300_0
    - xorg-renderproto 0.11.1 h7f98852_1002
    - xorg-xextproto 7.3.0 h0b41bf4_1003
    - xorg-xproto 7.0.31 h7f98852_1007
    - xz 5.2.6 h166bdaf_0
    - yaml 0.2.5 h7f98852_2
    - yq 3.2.2 pyhd8ed1ab_0
    - zlib 1.2.13 hd590300_5
    - zstd 1.5.2 hfc55251_7
  run:
    - bioconductor-singlecellexperiment >=1.22.0,<1.23.0
    - r-base >=4.3,<4.4.0a0
    - r-ggplot2
    - r-matrix
    - r-matrixstats
    - r-nmf
    - r-nnls
test:
  commands:
    - $R -e "library('SPOTlight')"
about:
  description: '`SPOTlight`provides a method to deconvolute spatial transcriptomics
    spots using a seeded NMF approach along with visualization tools to assess the
    results. Spatially resolved gene expression profiles are key to understand tissue
    organization and function. However, novel spatial transcriptomics (ST) profiling
    techniques lack single-cell resolution and require a combination with single-cell
    RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets.
    Leveraging the strengths of both data types, we developed SPOTlight, a computational
    tool that enables the integration of ST with scRNA-seq data to infer the location
    of cell types and states within a complex tissue. SPOTlight is centered around
    a seeded non-negative matrix factorization (NMF) regression, initialized using
    cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute
    ST capture locations (spots).'
  home: https://bioconductor.org/packages/3.17/bioc/html/SPOTlight.html
  license: GPL-3
  license_file: /opt/conda/conda-bld/bioconductor-spotlight_1689765065259/_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: '`SPOTlight`: Spatial Transcriptomics Deconvolution'
extra:
  copy_test_source_files: true
  final: true
