opm: Analysing Phenotype Microarray and Growth Curve Data

Tools for analysing OmniLog(R) and MicroStation(TM) phenotype microarray (PM) data as produced by the devices distributed by BIOLOG Inc. as well as similar kinds of data such as growth curves. Major facilities are plotting data, accurately estimating curve parameters, comparing and discretising data, creating phylogenetic formats and reports for taxonomic journals, drawing the PM analysis results in biochemical pathway graphs optionally including genome annotations, running multiple comparisons of means, easy interaction with powerful feature-selection approaches, integrating metadata, using the YAML format for the storage of data and metadata, batch conversion of large numbers of files, and database I/O.

AuthorMarkus Goeker, with contributions by Benjamin Hofner, Lea A.I. Vaas, Johannes Sikorski, Maria del Carmen Montero Calasanz, Jan P. Meier-Kolthoff, Nora Buddruhs and Anne Fiebig
Date of publication2016-11-14 17:03:08
MaintainerMarkus Goeker <markus.goeker@dsmz.de>
LicenseGPL (>= 2)
Version1.3.64
http://opm.dsmz.de/

View on R-Forge

Man pages

aggregated: Get aggregated data

annotated: Create vector or matrix with substrate annotation

as.data.frame: Create data frame

batch_opm: Batch-convert PM data

boccuto_et_al: Autism cell-line example data set

bracket: Select subset

bracket.set: Assign subset

c: Combination and addition of plates

ci_plot: Plot point estimates with CIs

collect_template: Input metadata

csv_data: Information from input CSV file

dim: Get dimensions

discrete: Discretisation functions

discretized: Get discretised data

do_aggr: Aggregate kinetics using curve-parameter estimation

do_disc: Discretise curve parameters

duplicated: Determine duplicated plates

explode_dir: Helper functions for file input and output

extract: Extract aggregated values and/or metadata

find_substrate: Identify substrates or positions

has_aggr: Are aggregated or discretised data present?

heat_map: Heat map

html_args: HTML formatting and output label generation

include_metadata: Add or map metadata or edit them by hand

infix.k: Query metadata keys

infix.q: Query metadata

kmeans: Work with k-means results

level_plot: Level plot

max: Overall or minimal maximum

measurements: Stored measurements

merge: Merge or split plates

metadata: Get metadata

metadata.set: Replace metadata

OPM: Real classes of the 'opm' package

OPM_DB: Classes for 'opm' database I/O

opm_dbput: Database I/O for 'opm'

opm_files: Files and colour sets used by the package

opm_mcp: Multiple comparison of group means

opm_opt: Global 'opm' options

opm.package: The 'opm' package

opms.function: OPMS constructor

opmx.function: Convert user-defined objects to OPMX

parallel_plot: Parallel plot

phylo_data: Export phylogenetic data

plates: Get available plates or apply function to them

plate_type: Plate type displayed or modified, registered or deleted

potato: Potato cell-line growth data set

radial_plot: Radial plot

read_opm: Read multiple PM files at once or read single PM file

run_kmeans: Conduct k-means partitioning

separate: Regularly split character vectors if possible

set_spline_options: Spline options

sort: Sort, unify, revert or repeat OPMS objects

subset: Select a subset of the plates (or time points)

substrate_info: Provide information on substrates

summary: Summarise OPMX or MOPMX objects

to_yaml: Convert to YAML

vaas_4: Example data sets from Vaas et al. (2012)

wells: Listing of well names

WMD: Virtual classes of the 'opm' package

xy_plot: X-Y plot

Files in this package

opm/COPYING
opm/ChangeLog
opm/DESCRIPTION
opm/NAMESPACE
opm/NEWS
opm/R
opm/R/aggregation-aux.R opm/R/aggregation.R opm/R/auxiliary-aux.R opm/R/auxiliary.R opm/R/classes-aux.R opm/R/classes.R opm/R/combination-aux.R opm/R/combination.R opm/R/constants.R opm/R/conversion-aux.R opm/R/conversion.R opm/R/data.R opm/R/dbio-aux.R opm/R/dbio.R opm/R/discretization.R opm/R/getter.R opm/R/imports.R opm/R/io-aux.R opm/R/io.R opm/R/kmeans-aux.R opm/R/kmeans.R opm/R/metadata.R opm/R/multcomp-aux.R opm/R/multcomp.R opm/R/naming-aux.R opm/R/naming.R opm/R/package.R opm/R/phylogeny-aux.R opm/R/phylogeny.R opm/R/plate-map.R opm/R/plotting-aux.R opm/R/plotting.R opm/R/splinefit-aux.R opm/R/substrate-info.R opm/R/testing-aux.R opm/R/well-map.R
opm/build
opm/build/vignette.rds
opm/data
opm/data/boccuto_et_al.rda
opm/data/potato.rda
opm/data/vaas_1.rda
opm/data/vaas_4.rda
opm/demo
opm/demo/00Index
opm/demo/MongoDB-IO.R
opm/demo/MySQL-IO.R
opm/demo/PostgreSQL-IO.R
opm/demo/SQLite-IO.R
opm/demo/cluster-with-pvalues.R
opm/demo/custom-PCA.R
opm/demo/distinguish-curve-topologies.R
opm/demo/identify-positive-reactions.R
opm/demo/multiple-plate-types.R
opm/demo/phenotype-vs-genotype.R
opm/demo/workshop-part-1.R
opm/demo/workshop-part-2.R
opm/demo/workshop-part-3.R
opm/demo/workshop-part-4.R
opm/demo/workshop-part-5.R
opm/inst
opm/inst/CITATION
opm/inst/auxiliary
opm/inst/auxiliary/001_rdbms_drop.sql
opm/inst/auxiliary/002_rdbms_create.sql
opm/inst/auxiliary/003_rdbms_delete.sql
opm/inst/auxiliary/styles_1.css
opm/inst/doc
opm/inst/doc/opm-growth-curves.Rnw
opm/inst/doc/opm-growth-curves.pdf
opm/inst/doc/opm-substrates.Rnw
opm/inst/doc/opm-substrates.pdf
opm/inst/doc/opm-tutorial.Rnw
opm/inst/doc/opm-tutorial.pdf
opm/inst/scripts
opm/inst/scripts/run_opm.R
opm/inst/testdata
opm/inst/testdata/Example_1.csv.xz
opm/inst/testdata/Example_2.csv.xz
opm/inst/testdata/Example_3.csv.xz
opm/inst/testdata/Example_Ecoplate.csv.xz
opm/inst/testdata/Example_ID_run.csv.xz
opm/inst/testdata/Example_LIMS_Export.exl.xz
opm/inst/testdata/Example_Old_Style_1.csv.xz
opm/inst/testdata/Example_Old_Style_2.csv.xz
opm/inst/testdata/Example_Old_Style_3.csv.xz
opm/inst/testdata/Example_Old_Style_Multiple.csv.xz
opm/inst/testdata/Example_Perkin_Elmer.txt.xz
opm/inst/testdata/Example_TECAN.txt.xz
opm/inst/tests
opm/inst/tests/test_aggregation-aux.R
opm/inst/tests/test_aggregation.R
opm/inst/tests/test_auxiliary-aux.R
opm/inst/tests/test_auxiliary.R
opm/inst/tests/test_classes-aux.R
opm/inst/tests/test_classes.R
opm/inst/tests/test_combination-aux.R
opm/inst/tests/test_combination.R
opm/inst/tests/test_constants.R
opm/inst/tests/test_conversion-aux.R
opm/inst/tests/test_conversion.R
opm/inst/tests/test_data.R
opm/inst/tests/test_dbio-aux.R
opm/inst/tests/test_dbio.R
opm/inst/tests/test_discretization.R
opm/inst/tests/test_getter.R
opm/inst/tests/test_imports.R
opm/inst/tests/test_io-aux.R
opm/inst/tests/test_io.R
opm/inst/tests/test_kmeans-aux.R
opm/inst/tests/test_kmeans.R
opm/inst/tests/test_metadata.R
opm/inst/tests/test_multcomp-aux.R
opm/inst/tests/test_multcomp.R
opm/inst/tests/test_naming-aux.R
opm/inst/tests/test_naming.R
opm/inst/tests/test_package.R
opm/inst/tests/test_phylogeny-aux.R
opm/inst/tests/test_phylogeny.R
opm/inst/tests/test_plate-map.R
opm/inst/tests/test_plotting-aux.R
opm/inst/tests/test_plotting.R
opm/inst/tests/test_splinefit-aux.R
opm/inst/tests/test_substrate-info.R
opm/inst/tests/test_testing-aux.R
opm/inst/tests/test_well-map.R
opm/man
opm/man/OPM.Rd opm/man/OPM_DB.Rd opm/man/WMD.Rd opm/man/aggregated.Rd opm/man/annotated.Rd opm/man/as.data.frame.Rd opm/man/batch_opm.Rd opm/man/boccuto_et_al.Rd opm/man/bracket.Rd opm/man/bracket.set.Rd opm/man/c.Rd opm/man/ci_plot.Rd opm/man/collect_template.Rd opm/man/csv_data.Rd opm/man/dim.Rd opm/man/discrete.Rd opm/man/discretized.Rd opm/man/do_aggr.Rd opm/man/do_disc.Rd opm/man/duplicated.Rd opm/man/explode_dir.Rd opm/man/extract.Rd opm/man/find_substrate.Rd opm/man/has_aggr.Rd opm/man/heat_map.Rd opm/man/html_args.Rd opm/man/include_metadata.Rd opm/man/infix.k.Rd opm/man/infix.q.Rd opm/man/kmeans.Rd opm/man/level_plot.Rd opm/man/max.Rd opm/man/measurements.Rd opm/man/merge.Rd opm/man/metadata.Rd opm/man/metadata.set.Rd opm/man/opm.package.Rd opm/man/opm_dbput.Rd opm/man/opm_files.Rd opm/man/opm_mcp.Rd opm/man/opm_opt.Rd opm/man/opms.function.Rd opm/man/opmx.function.Rd opm/man/parallel_plot.Rd opm/man/phylo_data.Rd opm/man/plate_type.Rd opm/man/plates.Rd opm/man/potato.Rd opm/man/radial_plot.Rd opm/man/read_opm.Rd opm/man/run_kmeans.Rd opm/man/separate.Rd opm/man/set_spline_options.Rd opm/man/sort.Rd opm/man/subset.Rd opm/man/substrate_info.Rd opm/man/summary.Rd opm/man/to_yaml.Rd opm/man/vaas_4.Rd opm/man/wells.Rd opm/man/xy_plot.Rd
opm/tests
opm/tests/run-all.R
opm/vignettes
opm/vignettes/opm-growth-curves.Rnw
opm/vignettes/opm-substrates.Rnw
opm/vignettes/opm-tutorial.Rnw

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