Package: clusnalyst 0.1.0

clusnalyst: Point-and-Click Cluster Analysis of Molecular and Trait Data

A 'shiny' application and a set of plain R functions for clustering samples from dominant markers, SNP genotypes (CSV, VCF or HapMap), quantitative or mixed traits, and DNA or protein sequences. It computes distance matrices, builds trees by UPGMA, WPGMA, single, complete or Ward linkage, neighbour joining or BIONJ, and checks them with marker bootstrap support (Felsenstein 1985 <doi:10.1111/j.1558-5646.1985.tb00420.x>), cophenetic correlation, average silhouette width, the gap statistic and Mantel tests. It also offers principal coordinates and principal components, k-means and partitioning around medoids, and exports a self-contained HTML report and an R script that reproduces the analysis.

Authors:Ebenezer Ogoe [aut, cre, cph], Michael Obeng [aut], Stephen Amoako [aut]

clusnalyst_0.1.0.tar.gz
clusnalyst_0.1.0.zip(r-4.7-any)clusnalyst_0.1.0.zip(r-4.6-any)clusnalyst_0.1.0.zip(r-4.5-any)
clusnalyst_0.1.0.tgz(r-4.6-any)clusnalyst_0.1.0.tgz(r-4.5-any)
clusnalyst_0.1.0.tar.gz(r-4.7-any)clusnalyst_0.1.0.tar.gz(r-4.6-any)
clusnalyst_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clusnalyst/json (API)

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

Bug tracker:https://github.com/ebenogoe/clusnalyst/issues

Pkgdown/docs site:https://ebenogoe.github.io

On CRAN:

Conda:

cluster-analysisphylogeneticsplant-breedingshiny

1.70 score 50 exports 121 dependencies

Last updated from:026a65b73d (on main). Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK179
source / vignettesOK246
linux-releaseOK205
macos-releaseOK112
macos-oldrelOK131
windows-develOK111
windows-releaseOK133
windows-oldrelOK109
wasm-releaseOK146

Exports:align_sequencesattach_metadatabootstrap_treebuild_reportbuild_scriptbuild_treecl_paletteclusnalyst_democompute_distanceconsensus_treecophenetic_corcophenetic_tabledata_typesdefault_distancedefault_settingsdemo_infodetect_formatdistance_choicesfilter_datagenotypes_to_dosageguess_typehas_numericload_sessionmantel_testmetadata_distanceoptimal_kordinatepartitionplot_heatmapplot_kplot_mantelplot_ordinationplot_qcplot_screeplot_supportplot_treeqc_summaryread_fastaread_hapmapread_markersread_metadataread_second_matrixread_vcfrun_analysisrun_appsample_namessave_sessionsilhouette_meaningtheme_clusnalysttree_choices

Dependencies:ade4apeaplotassertthatattemptbase64encBiocGenericsBiostringsbsiconsbslibcachemcellrangerciceronecliclustercodetoolscommonmarkconfigcpp11crayondigestdplyrevaluatefarverfastmapfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggfunggiraphggplot2ggplotifyggtreegluegolemgridGraphicsgtablehighrhmshtmltoolshtmlwidgetshttpuvIRangesisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisememusemgcvmimemsaMultipleAlignmentnlmeotelpatchworkpermutepillarpinfsc50pixmappkgconfigprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloreactablereactRreadxlrematchrlangrmarkdownS4VectorsS7sassscalessegmentedSeqinfoseqinrshinysourcetoolsspstringistringrsvglitesystemfontstextshapingtibbletidyrtidyselecttidytreetinytextreeioutf8vcfRvctrsveganviridisLitewithrwritexlxfunxtableXVectoryamlyulab.utils

Readme and manuals

Help Manual

Help pageTopics
Align sequences with the msa packagealign_sequences
Attach metadata to a datasetattach_metadata
Bootstrap support for a treebootstrap_tree
Write a self-contained HTML reportbuild_report
Write an R script that repeats an analysisbuild_script
Build a tree from a distance matrixbuild_tree
Colours for groupscl_palette
Compute a distance matrixcompute_distance
Majority-rule consensus of bootstrap treesconsensus_tree
Cophenetic correlation of a treecophenetic_cor
Compare tree methods by cophenetic correlationcophenetic_table
Data types Clusnalyst works withdata_types
Default distance for a datasetdefault_distance
Default analysis settingsdefault_settings
Demo datasetsclusnalyst_demo demo_info
Guess the format of a data filedetect_format
Distance measures available for a data typedistance_choices
Filter markers, traits or sequencesfilter_data
Convert letter genotypes to allele dosagesgenotypes_to_dosage
Guess the data type of a tableguess_type
Can PCA or k-means be used on this dataset?has_numeric
Mantel test between two distance matricesmantel_test
Distances from numeric metadata columnsmetadata_distance
Choose the number of clustersoptimal_k
Principal coordinates or principal componentsordinate
Split samples into groupspartition
Heatmap of a distance matrixplot_heatmap
Plot the cluster-number diagnosticsplot_k
Plot two distance matrices against each otherplot_mantel
Plot an ordinationplot_ordination
Plot quality-check summariesplot_qc
Scree plot of an ordinationplot_scree
Plot bootstrap support valuesplot_support
Plot a treeplot_tree
Quality summary of a datasetqc_summary
Read a FASTA fileread_fasta
Read a HapMap genotype fileread_hapmap
Read a data file into a Clusnalyst datasetread_markers
Read a sample metadata tableread_metadata
Read a second matrix for a Mantel testread_second_matrix
Read a VCF file as SNP dosagesread_vcf
Run a whole analysis from settingsrun_analysis
Run the Clusnalyst apprun_app
Sample names of a Clusnalyst datasetsample_names
Save and restore an analysis sessionload_session save_session
How to read an average silhouette widthsilhouette_meaning
ggplot2 theme used by Clusnalysttheme_clusnalyst
Tree-building methodstree_choices