パッケージ: seer (1.1.4-7)
genomic sequence element (kmer) enrichment analysis
Bacterial genomes vary extensively in terms of both gene content and gene sequence - this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. SEER provides a computationally scalable and widely applicable statistical method for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable- length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogen Streptococcus pneumoniae, SEER identifies relevant previously characterised resistance determinants for several antibiotics.
その他の seer 関連パッケージ
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- dep: libarmadillo11 (>= 1:11.4.2+dfsg)
- C++ の簡素化した線形代数ライブラリ
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- dep: libblas3
- 基本線形代数のリファレンス実装 - 共有ライブラリ
- または libblas.so.3
- 以下のパッケージによって提供される仮想パッケージです: libatlas3-base, libblas3, libblis4-openmp, libblis4-pthread, libblis4-serial, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial
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- dep: libboost-program-options1.74.0 (>= 1.74.0)
- C++ 用プログラムオプションライブラリ
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- dep: libc6 (>= 2.34)
- GNU C ライブラリ: 共有ライブラリ
以下のパッケージによって提供される仮想パッケージでもあります: libc6-udeb
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- dep: libgcc-s1 (>= 7)
- GCC 共有ライブラリ
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- dep: libgzstream0 (>= 1.5+dfsg)
- provide functionality of zlib C-library in a C++ iostream
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- dep: libhdf5-103-1
- HDF5 C runtime files - serial version
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- dep: libstdc++6 (>= 12.2.0-9)
- GNU 標準 C++ ライブラリ v3
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- dep: libtext-csv-perl
- comma-separated values manipulator (using XS or PurePerl)
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- dep: zlib1g (>= 1:1.1.4)
- 圧縮ライブラリ - ランタイム
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- sug: fsm-lite
- frequency-based string mining (lite)