nuget
SMRUCC.genomics.Analysis.Metagenome 1.0.9753.40023.
01 Namespaces
SMRUCC.genomics.Analysis.Metagenome
| Type | Summary | Members |
|---|---|---|
| ACE | Ace – the ACE estimator (http://www.mothur.org/wiki/Ace)；用来估计群落中OTU 数目的指数，由Chao 提出，是生态学中估计物种总数的常用指数之一 | 0 |
| BIOM | 生成BIOM数据模型 | 4 |
| BIOMExtensions | 1 | |
| CoreMicrobiomeCalculator | 从一个OTU相对丰度表格中筛选出核心微生物群落，“跨样本/全局维度”的普遍性+丰度筛选，找的是“核心种” | 0 |
| Enterotype | Protocol module to produce enterotype clusters | 2 |
| ITaxonomyAbundance | [id, ncbi_taxid, expression_value] | 0 |
| MeganImports | Megan Csv imports | 5 |
| MetagenomicsBenchmark | 算法比较评估模块 | 4 |
| OTU | 2 | |
| OTUTable | OTU table (sequence count table) A OTU table contains the number of sequences that are observed for each taxonomic unit (OTUs) in each samples. | 5 |
| OTUTableBuilder | 1 | |
| RankAbundance | Rank Abundance曲线 | 2 |
| RankLevelView | samples data aggregate in a specific taxonomy rank | 3 |
| RelativeStatics | 6 | |
| SILVA_OTU | 3 | |
| SILVABuild | 1 | |
| ToolScore | 单个工具的评估得分 | 8 |
| UniFracCalculator | 2 |
SMRUCC.genomics.Analysis.Metagenome.BEBaC
| Type | Summary | Members |
|---|---|---|
| CrudeClustering | 2 | |
| I3Mers | Where a 3-mer means 3 consecutive DNA bases ranging from AAA to TTT. | 64 |
| PosteriorProbability | 3 | |
| VectorAPI | 2 |
SMRUCC.genomics.Analysis.Metagenome.gast
| Type | Summary | Members |
|---|---|---|
| ARGV | gast -in input_fasta -ref reference_uniques_fasta -rtax reference_dupes_taxonomy [-mp min_pct_id] [-m majority] -out output_file | 19 |
| gast_tools | 5 | |
| GastAPI | compares trimmed sequences against a reference database for assigning taxonomy, reads a fasta file of trimmed 16S sequences, compares each sequence to a Set Of similarly trimme… | 8 |
| gastOUT | The gast script OTU count result table | 4 |
| Names | .names 相当于一个OTU数据 | 1 |
| SUBROUTINES | SUBROUTINES | 0 |
| Taxonomy | Create taxonomic objects, Return classes Or full text Of a taxonoDim Object, Calculate consensus Of an array Of taxonomic objects. | 8 |
| TaxonomyTree | a taxonomy tree node | 2 |
| TreeBuilder | 1 |
SMRUCC.genomics.Analysis.Metagenome.GCModeller.FileSystem
| Type | Summary | Members |
|---|---|---|
| FileSystem | 16 |
SMRUCC.genomics.Analysis.Metagenome.GCModeller.FileSystem.KEGG
| Type | Summary | Members |
|---|---|---|
| Directories | 1 |
SMRUCC.genomics.Analysis.Metagenome.GCModeller.FileSystem.RegPrecise
| Type | Summary | Members |
|---|---|---|
| Directories | 2 |
SMRUCC.genomics.Analysis.Metagenome.greengenes
| Type | Summary | Members |
|---|---|---|
| Extensions | 2 | |
| otu_taxonomy | otu id mappingg to taxonomy lineage information | 2 |
SMRUCC.genomics.Analysis.Metagenome.Kmers
| Type | Summary | Members |
|---|---|---|
| AbundanceEstimate | 8 | |
| Classifier | 2 | |
| DatabaseReader | 4 | |
| DatabaseWriter | 3 | |
| Extensions | 1 | |
| KmerBloomFilter | kmer bloom filter of a specific genome | 2 |
| KmerFilter | 3 | |
| KmerHashIndexFilter | 1 | |
| KmersDatabase | 7 | |
| KmerSeed | 4 | |
| KmerSource | 4 | |
| KmerWriter | 9 | |
| PriorProbabilityBuilder | 4 | |
| SequenceCollection | 6 | |
| SequenceSource | source information of the target genome source sequence | 7 |
| ShardingReader | 3 | |
| ShardingWriter | 8 |
SMRUCC.genomics.Analysis.Metagenome.Kmers.Kraken2
| Type | Summary | Members |
|---|---|---|
| Bracken | the bracken abundance table | 0 |
| KrakenOutputRecord | 用于存储 --output 文件中每一行的数据，这个文件详细列出了每一条序列（read）的分类结果。每一行对应一条 read。 | 12 |
| KrakenParser | 2 | |
| KrakenReportRecord | 用于存储 --report 文件中每一行的数据。这个文件提供了整个样本的分类汇总统计，非常直观。 | 6 |
| ReportFilter | 3 | |
| TaxonomyTreeBuilder | 2 |
SMRUCC.genomics.Analysis.Metagenome.Settings
SMRUCC.genomics.Analysis.Metagenome.Settings.Programs
SMRUCC.genomics.Analysis.Metagenome.Settings.Programs.IDE
| Type | Summary | Members |
|---|---|---|
| Languages | Enum the mainly used language. | 8 |
SMRUCC.genomics.Analysis.Metagenome.UniFracCalculator
| Type | Summary | Members |
|---|---|---|
| PhylogeneticBranch | 定义系统发育树分支结构 | 2 |
SMRUCC.genomics.Analysis.Metagenome.UPGMATree
| Type | Summary | Members |
|---|---|---|
| NodeLayout | 用于缓存每个节点的极坐标布局信息 | 0 |
| Taxa | Taxonomy tree model | 1 |
| TreeDrawer | 5 | |
| UPGMATree | 基于矩阵数据结构（两两比较的得分/距离矩阵），最常用的从零构建进化树的算法是 UPGMA（Unweighted Pair Group Method with Arithmetic Mean）算法。 UPGMA 是一种自底向上的聚类算法，它假设分子钟假说（即所有物种的进化速率相同），最终生成一棵有根树。本质上是基于平均连接值得层次聚类树。 > http… | 1 |
SMRUCC.genomics.Analysis.Metagenome.ZetaDiversity
| Type | Summary | Members |
|---|---|---|
| ZetaAnalysisResult | Complete result container for zeta diversity analysis. | 18 |
| ZetaDiversityAnalysis | Zeta Diversity Analysis Module # # Based on: Hui, C., & McGeoch, M. | 27 |
| ZetaFitResult | Container for zeta diversity model fitting results. | 10 |
| ZetaNullModelResult | Container for null model permutation test results. | 6 |