软件包：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.
其他与 seer 有关的软件包
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- dep: libblas3
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- 或者 libblas.so.3
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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 语言运行库：共享库
同时作为一个虚包由这些包填实： libc6-udeb
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- dep: libgcc-s1 (>= 4.5)
- GCC 支持库
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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 标准 C++ 库，第3版
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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)
- 压缩库 - 运行时
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- sug: fsm-lite
- frequency-based string mining (lite)