套件：seer（1.1.4-8）
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.
其他與 seer 有關的套件
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- dep: libarmadillo14 (>= 1:14.0.1+dfsg)
- streamlined C++ linear algebra library
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- dep: libblas3
- Basic Linear Algebra Reference implementations, shared library
- 或者 libblas.so.3
- 本虛擬套件由這些套件填實： libatlas3-base, libblas3, libblis4-openmp, libblis4-pthread, libblis4-serial, libopenblas0-openmp, libopenblas0-pthread, libopenblas0-serial
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- dep: libboost-program-options1.83.0 (>= 1.83.0)
- program options library for C++
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- dep: libc6 (>= 2.38)
- GNU C 函式庫：共用函式庫
同時作為一個虛擬套件由這些套件填實： libc6-udeb
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- dep: libgcc-s1 (>= 3.0)
- GCC 支援函式庫
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- dep: libgzstream0 (>= 1.5+dfsg)
- provide functionality of zlib C-library in a C++ iostream
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- dep: libhdf5-103-1t64
- HDF5 C runtime files - serial version
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- dep: libstdc++6 (>= 14)
- GNU Standard C++ Library 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)
- 壓縮函式庫 - 跑程式時用(runtime)
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- sug: fsm-lite
- frequency-based string mining (lite)