Summary | Important note | How to obtain phylogentic placement file suitable for analysis with BoSSA ? | Exploration of a reference package | Loading the example data | Some plots | Subsetting the pplace object | Conversion | To a table | To a contingency matrix | To a taxonomy | Make a phyloseq object | Citation | Other resources | On phylogenetic placements | Other R package with a related topic | R packages used by BoSSA
Package: BoSSA 3.7
BoSSA: A Bunch of Structure and Sequence Analysis
Reads and plots phylogenetic placements.
Authors:
BoSSA_3.7.tar.gz
BoSSA_3.7.zip(r-4.7-any)BoSSA_3.7.zip(r-4.6-any)BoSSA_3.7.zip(r-4.5-any)
BoSSA_3.7.tgz(r-4.6-any)BoSSA_3.7.tgz(r-4.5-any)
BoSSA_3.7.tar.gz(r-4.7-any)BoSSA_3.7.tar.gz(r-4.6-any)
BoSSA_3.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BoSSA/json (API)
| # Install 'BoSSA' in R: |
| install.packages('BoSSA', repos = c('https://lefeup.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- pplace - A placement object as obtained with the read_sqlite function
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:4610ba845c. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 159 | ||
| source / vignettes | OK | 178 | ||
| linux-release-x86_64 | OK | 155 | ||
| macos-release-arm64 | OK | 177 | ||
| macos-oldrel-arm64 | OK | 249 | ||
| windows-devel | OK | 118 | ||
| windows-release | OK | 111 | ||
| windows-oldrel | OK | 118 | ||
| wasm-release | OK | 116 |
Exports:circular_treeplot.jplaceplot.pplacepplace_to_matrixpplace_to_tablepplace_to_taxonomyprint.jplaceprint.pplaceprint.protdbread_jplaceread_protdbread_sqliterefpkgsub_pplacewrite_jplace
Dependencies:apebitbit64blobcachemclicpp11DBIdigestfastmapfastmatchgenericsglueigraphjsonlitelatticelifecyclemagrittrMatrixmemoisenlmephangornpkgconfigplotrixquadprogRcpprlangRSQLitevctrs
Example of placement analysis using BoSSA
Last update: 2020-10-20
Started: 2017-05-09
Reference package construction from scratch
Important notice | Summary | The polerovirus example | Loading the required packages | How many polerovirus sequences are available on NCBI ? | Download all these sequences | Get the genbank informations in XML format | Extract the fasta from the XML | Extract the taxonomy from the XML | Alignement and phylogeny | The Taxonomy | Download the polerovirus taxonomy IDs | The information file | Create the refpkg using taxit | Check the refpkg using rppr | Refpkg stats using BoSSA | Subsample the refpkg | Citation | Other resources | On phylogenetic placements | Other R package with a related topic | On krona charts | R packages used by BoSSA
Last update: 2020-10-20
Started: 2017-05-09
Circular tree plot
Cicular tree | Loading of the required packages | Let's use a random tree | Here is the "inside-out" circular tree plot | Plotting interactions | Citation
Last update: 2018-09-25
Started: 2018-06-25
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A Bunch of Structure and Sequence Analysis | BoSSA-package BoSSA |
| Plot an inside-out circular tree | circular_tree |
| Plot a pplace or jplace object | plot.jplace plot.pplace |
| A placement object as obtained with the read_sqlite function | pplace |
| Pplace to contingency matrix | pplace_to_matrix |
| Merge the multiclass and the placement table of pplace object | pplace_to_table |
| Convert a pplace object to a taxonomy table | pplace_to_taxonomy |
| Compact display of pplace and jplace objects | print.jplace print.pplace |
| Compact display of protdb object | print.protdb |
| Read a jplace file | read_jplace |
| Read Protein Data Bank (PDB) file | read_protdb |
| Read a pplacer/guppy sqlite file | read_sqlite |
| Summary data and plots for reference packages | refpkg |
| Subsets a pplace object | sub_pplace |
| Write a jplace or pplace object to the disk | write_jplace |
