Package: tidyestimate 1.1.1.9000

tidyestimate: A Tidy Implementation of 'ESTIMATE'

The 'ESTIMATE' package infers tumor purity from expression data as a function of immune and stromal infiltrate, but requires writing of intermediate files, is un-pipeable, and performs poorly when presented with modern datasets with current gene symbols. 'tidyestimate' a fast, tidy, modern reimagination of 'ESTIMATE' (2013) <doi:10.1038/ncomms3612>.

Authors:Kai Aragaki [aut, cre], Paul Roebuck [cph], Kosuke Yoshihara [aut], Rahulsimham Vegesna [aut], Hoon Kim [aut], Roel Verhaak [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tidyestimate/json (API)

# Install 'tidyestimate' in R:

install.packages('tidyestimate', repos = c('https://kaiaragaki.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kaiaragaki/tidyestimate/issues

Datasets:

common_genes - Genes shared between six expression platforms
gene_sets - Gene sets to infer tumor stromal and immune infiltration
ov - Ovarian cancer tumor RNA expression
purity_data_affy - Affymetrix data used to train ESTIMATE algorithm

On CRAN:

cancer-genomics tidy

5.28 score 18 stars 21 scripts 356 downloads 3 exports 27 dependencies

Last updated from:7f98f860d3. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	135
source / vignettes	OK	174
linux-release-x86_64	OK	126
macos-release-arm64	OK	86
macos-oldrel-arm64	OK	104
windows-devel	OK	102
windows-release	OK	100
windows-oldrel	OK	84
wasm-release	OK	109

Exports:estimate_score filter_common_genes plot_purity

Dependencies:cli cpp11 dplyr farver generics ggplot2 ggrepel glue gtable isoband labeling lifecycle magrittr pillar pkgconfig R6 RColorBrewer Rcpp rlang S7 scales tibble tidyselect utf8 vctrs viridisLite withr

Using tidyestimate

Introduction | Use

Rendered fromusing-tidyestimate.Rmdusingknitr::rmarkdown

Last update: 2021-06-15
Started: 2021-06-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Genes shared between six expression platforms	common_genes
Infer tumor purity using the ESTIMATE algorithm	estimate_score
Remove non-common genes from data frame	filter_common_genes
Gene sets to infer tumor stromal and immune infiltration	gene_sets
Ovarian cancer tumor RNA expression	ov
Plot Affymetrix purity scores against ESTIMATE study purity scores	plot_purity
Affymetrix data used to train ESTIMATE algorithm	purity_data_affy
tidyestimate: A modern implementation of the ESTIMATE algorithm	tidyestimate