Package: greatR 2.1.0

greatR: Gene Registration from Expression and Time-Courses in R

A tool for registering (aligning) gene expression profiles between reference and query data.

Authors:Ruth Kristianingsih [aut, cre]

greatR_2.1.0.tar.gz
greatR_2.1.0.zip(r-4.7-any)greatR_2.1.0.zip(r-4.6-any)greatR_2.1.0.zip(r-4.5-any)
greatR_2.1.0.tgz(r-4.6-any)greatR_2.1.0.tgz(r-4.5-any)
greatR_2.1.0.tar.gz(r-4.7-any)greatR_2.1.0.tar.gz(r-4.6-any)
greatR_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
greatR/json (API)

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

Bug tracker:https://github.com/ruthkr/greatr/issues

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

On CRAN:

Conda:

4.41 score 1 stars 13 scripts 337 downloads 3 exports 36 dependencies

Last updated from:f577b51aea. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK168
source / vignettesOK213
linux-releaseOK132
macos-releaseOK132
macos-oldrelOK163
windows-develOK76
windows-releaseOK85
windows-oldrelOK83
wasm-releaseOK89

Exports:calculate_distanceget_approximate_stretchregister

Dependencies:clicodetoolscolorspacecpp11data.tabledigestfarverfurrrfutureggplot2globalsgluegtableisobandlabelinglatticelifecyclelistenvmagrittrMatrixneldermeadoptimbaseoptimizationoptimsimplexparallellypatchworkpurrrR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr

Input data requirements
A single data frame input | A list of data frames as an input | A list of vectors as an input
Rendered fromdata-requirement.Rmdusingknitr::rmarkdown

Last update: 2024-03-24
Started: 2023-02-22

Processing results
Summarising registration results | Plot distribution of registration parameters | Plotting registration results | Analysing similarity of expression profiles over time before and after registering | Calculate sample distance | Plot heatmap of sample distances
Rendered fromprocess-results.Rmdusingknitr::rmarkdown

Last update: 2024-03-24
Started: 2024-03-24

Registering data
Using data frame input | Loading sample data | Registering the data | Registration results | Using other inputs
Rendered fromregister-data.Rmdusingknitr::rmarkdown

Last update: 2024-03-24
Started: 2021-10-19

Registering data without optimisation
Load sample data | Registering without optimisation | Registering multiple gene with different pre-defined registration parameters
Rendered fromregister-data-manually.Rmdusingknitr::rmarkdown

Last update: 2024-03-24
Started: 2023-02-22