| kmer: KmerSeed | |
| kmer_bloom: KmerBloomFilter | kmer bloom filter of a specific genome |
| as.data.frame.bracken | Bracken: the bracken abundance table |
| as.data.frame.sequencesource | SequenceSource: source information of the target genome source sequence |
| as.data.frame.krakenoutputrecord | 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。 |
| as.data.frame.sequencehit | SequenceHit: |
| write.kmers_background | |
| read.kmers_background | |
| bayes_background | |
| read_seqid | |
| bloom_filters | |
| bloom_vector | |
| make_vector | make vector embedding |
| make_classify | just make reads classify of the fastq reads based on the k-mer distribution |
| benchmark | |
| MAG_classify | |
| bayes_estimate | |
| bayes_abundance | quantify of the metagenome community via kmers and bayes method |
| as.bloom_filter | cast the genomics sequence as kmer based bloom filter model |
| parse_kraken_output | Parse the reads annotation result generated from the kraken2 |
| make_seq_groups | |
| parse_kraken_report | |
| read.kraken2 | |
| read_brackens | |
| read.kraken2_reads | read reads annotation result generated from the kraken2 |
| hits_matrix | |
| filter_classification | filter the reads data that has the specific taxonomy id assignment. |
| filter_hostId | |
| kraken_data | extract the kraken2 quantify result data |
| filter_reads | usually be apply for host removal |
| seq_info | |
| taxonomy_expression | |
| kraken_seqs | extract gene/genomics sequences from genbank file for kraken2 sequence classification |