Package: microclass 1.2

microclass: Tools for taxonomic classification of prokaryotes

Functions for working with taxonomic classifications in R

Authors:Kristian Hovde Liland, Hilde Vinje, Lars Snipen

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microclass.pdf |microclass.html✨
microclass/json (API)

# Install 'microclass' in R:
install.packages('microclass', repos = c('https://larssnip.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/larssnip/microclass/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

35 exports 4 stars 1.87 score 26 dependencies 3 mentions 20 scripts 228 downloads

Last updated 11 months agofrom:3f3ac0ad10. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-win-x86_64WARNINGSep 08 2024
R-4.5-linux-x86_64WARNINGSep 08 2024
R-4.4-win-x86_64WARNINGSep 08 2024
R-4.4-mac-x86_64WARNINGSep 08 2024
R-4.4-mac-aarch64WARNINGSep 08 2024
R-4.3-win-x86_64WARNINGSep 08 2024
R-4.3-mac-x86_64WARNINGSep 08 2024
R-4.3-mac-aarch64WARNINGSep 08 2024

Exports:blastClassify16SblastDbase16Sbracken_read_reportbranch_list2qiimebranch_list2tablebranch_name2taxidbranch_prunebranch_retrievebranch_table2listbranch_taxid2nameclrgetClassgetDomaingetFamilygetGenusgetOrdergetPhylumgetTaggetTaxonomyKmerCountkraken2_read_reportkraken2_read_tablemicroclassmultinomClassifymultinomTrainrdpClassifyrdpTrainread_names_dmpread_nodes_dmpsetParallelsubset_cladesubset_treetaxMachinewrite_names_dmpwrite_nodes_dmp

Dependencies:clidata.tabledplyrfansigenericsgluelatticelifecyclemagrittrMatrixmicrocontaxmicroseqpillarpkgconfigR6RcppRcppEigenRcppParallelrlangstringistringrtibbletidyselectutf8vctrswithr

Introduction to microclass

Kristian Hovde Liland, Hilde Vinje and Lars Snipen

Rendered fromintro.Rmdusingknitr::rmarkdownon Sep 08 2024.

Last update: 2022-05-22
Started: 2017-08-10

Readme and manuals

Help Manual

Help pageTopics
Methods for 16S based taxonomic classification of prokaryotesmicroclass-package microclass
Classifying using BLASTblastClassify16S
Building a BLAST databaseblastDbase16S
Reads bracken reportsbracken_read_report
Branch list to QIIME formatbranch_list2qiime
Branch list na dtable conversionbranch_list2table branch_table2list
Filtering ranks in branchesbranch_prune
Retrieves branchesbranch_retrieve
Replace tax_id with namebranch_name2taxid branch_taxid2name branch_taxid2name,
Centred log-ratio transformclr
Extractor functions for QIIME taxonomygetClass getDomain getFamily getGenus getOrder getPhylum getTag getTaxonomy
K-mer countingKmerCount
Reads 'kraken2' reportskraken2_read_report
Reads raw 'kraken2' outputkraken2_read_table
Classifying with a Multinomial modelmultinomClassify
Training multinomial modelmultinomTrain
Classifying with the RDP classifierrdpClassify
Training the RDP classifierrdpTrain
Read and write the names.dmpread_names_dmp write_names_dmp
Read and write the nodes.dmpread_nodes_dmp write_nodes_dmp
Set number of parallel threadssetParallel
A small example data setsmall.16S
Subset the taxonomy tree from the rootsubset_clade
Subset the taxonomy tree from leavessubset_tree
Classifying 16S sequencestaxMachine