BoSSA: A Bunch of Structure and Sequence Analysis
Version 2.1

Reads and plots phylogenetic placements obtained using the 'pplacer' and 'guppy' softwares .

Authorpierre lefeuvre
Date of publication2017-05-09 21:26:36 UTC
Maintainerpierre lefeuvre <pierre.lefeuvre@cirad.fr>
LicenseGPL
Version2.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BoSSA")

Getting started

Package overview
Example of placement analysis using BoSSA
Reference package construction from scratch

Popular man pages

BoSSA-package: A Bunch of Structure and Sequence Analysis
plot.pplace: Plot a pplace object
pplace_to_taxonomy: Convert a pplace object to a taxonomy table
read_pdb: Read Protein Data Bank (PDB) file
read_sqlite: Read a pplacer/guppy sqlite file
refpkg: Summary data and plots for reference packages
sub_pplace: Subsets a pplace object
See all...

All man pages Function index File listing

Man pages

BoSSA-package: A Bunch of Structure and Sequence Analysis
plot.pplace: Plot a pplace object
pplace: A placement object as obtained with the read_sqlite function
pplace_to_matrix: Pplace to contingency matrix
pplace_to_table: Merge the multiclass and the placement table of pplace object
pplace_to_taxonomy: Convert a pplace object to a taxonomy table
print.pdb: Compact display of protdb object
print.pplace: Compact display of pplace object
read_pdb: Read Protein Data Bank (PDB) file
read_sqlite: Read a pplacer/guppy sqlite file
refpkg: Summary data and plots for reference packages
sub_pplace: Subsets a pplace object

Functions

BoSSA Man page
BoSSA-package Man page
get_edge Source code
plot.pplace Man page Source code
pplace Man page
pplace_to_matrix Man page Source code
pplace_to_table Man page Source code
pplace_to_taxonomy Man page Source code
print.pplace Man page Source code
print.protdb Man page Source code
read_jplace Source code
read_protdb Man page Source code
read_sqlite Man page Source code
refpkg Man page Source code
sub_pplace Man page Source code

Files

inst
inst/extdata
inst/extdata/polerovirus_from_genbank_MAFFT.tre
inst/extdata/example.refpkg
inst/extdata/example.refpkg/CONTENTS.json
inst/extdata/example.refpkg/bv_refdata.csv
inst/extdata/example.refpkg/RAxML_result.bv_refs_aln
inst/extdata/example.refpkg/tax_table.csv
inst/extdata/polerovirus.refpkg
inst/extdata/polerovirus.refpkg/polerovirus_taxonomy.csv
inst/extdata/polerovirus.refpkg/polerovirus_info.csv
inst/extdata/polerovirus.refpkg/CONTENTS.json
inst/extdata/polerovirus.refpkg/polerovirus_ROOTED.tre
inst/extdata/example.jplace
inst/extdata/1L2M.pdb
inst/extdata/polerovirus_taxonomy.csv
inst/extdata/example.sqlite
inst/doc
inst/doc/bossa-analysis.Rmd
inst/doc/bossa-refpkg.html
inst/doc/bossa-refpkg.R
inst/doc/bossa-refpkg.Rmd
inst/doc/bossa-analysis.R
inst/doc/bossa-analysis.html
NAMESPACE
data
data/pplace.rda
R
R/refpkg.R
R/plot.pplace.R
R/pplace_to_taxonomy.R
R/read_jplace.R
R/pplace_to_table.R
R/pplace_to_matrix.R
R/read_sqlite.R
R/read_pdb.R
R/get_edge.R
R/print.pplace.R
R/sub_pplace.R
R/print.pdb.R
vignettes
vignettes/bossa-analysis.Rmd
vignettes/bossa-refpkg.Rmd
MD5
build
build/vignette.rds
build/partial.rdb
DESCRIPTION
man
man/plot.pplace.Rd
man/read_sqlite.Rd
man/pplace_to_table.Rd
man/pplace_to_taxonomy.Rd
man/read_pdb.Rd
man/BoSSA-package.Rd
man/refpkg.Rd
man/print.pdb.Rd
man/print.pplace.Rd
man/sub_pplace.Rd
man/pplace_to_matrix.Rd
man/pplace.Rd
BoSSA documentation built on May 19, 2017, 10:24 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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