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dowser
View on CRAN: Click
here
Download and install dowser package within the R console
Install from CRAN:
install.packages("dowser")
Install from Github:
library("remotes")
install_github("cran/dowser")
Install by package version:
library("remotes")
install_version("dowser", "2.3")
Attach the package and use:
library("dowser")
Maintained by
Kenneth Hoehn
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-07-22
Latest Update: 2023-05-30
Description:
Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees.
Provides methods to 1) reconstruct unmutated ancestral sequences,
2) build B cell phylogenetic trees using multiple methods,
3) visualize trees with metadata at the tips,
4) reconstruct intermediate sequences,
5) detect biased ancestor-descendant relationships among metadata types
Workflow examples available at documentation site (see URL).
Citations:
Hoehn et al (2022) ,
Hoehn et al (2021) .
How to cite:
Kenneth Hoehn (2021). dowser: B Cell Receptor Phylogenetics Toolkit. R package version 2.3, https://cran.r-project.org/web/packages/dowser. Accessed 22 Dec. 2024.
Previous versions and publish date:
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imports, suggests or enhances
Complete documentation for dowser
Functions, R codes and Examples using
the dowser R package
Some associated functions: BiopsyTrees . ExampleAirr . ExampleClones . ExampleDbChangeo . ExampleMixedClones . ExampleMixedDb . IsotypeTrees . TimeTrees . airrClone-class . bootstrapTrees . buildClonalGermline . buildGermline . buildIgphyml . buildPML . buildPhylo . buildPratchet . buildRAxML . calcRF . collapseNodes . colorTrees . condenseTrees . correlationTest . createGermlines . downsampleClone . dowser-package . dowser . findSwitches . formatClones . getBootstraps . getDivergence . getGermline . getNodeSeq . getPalette . getSeq . getSubTaxa . getSubclones . getTrees . makeAirrClone . makeModelFile . maskCodons . maskSequences . plotTrees . readFasta . readIMGT . readLineages . readModelFile . reconIgPhyML . rerootTree . resolveLightChains . resolvePolytomies . runCorrelationTest . scaleBranches . stitchRegions . stitchVDJ . testPS . testSC . testSP . treesToPDF . writeLineageFile .
Some associated R codes: Classes.R . Clones.R . Data.R . Dowser.R . Germlines.R . Plotting.R . Statistics.R . TreeFunctions.R . zzz.R . Full dowser package functions and examples
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