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]

tidyestimate_1.1.1.9000.tar.gz
tidyestimate_1.1.1.9000.zip(r-4.7)tidyestimate_1.1.1.9000.zip(r-4.6)tidyestimate_1.1.1.9000.zip(r-4.5)
tidyestimate_1.1.1.9000.tgz(r-4.6-any)tidyestimate_1.1.1.9000.tgz(r-4.5-any)
tidyestimate_1.1.1.9000.tar.gz(r-4.7-any)tidyestimate_1.1.1.9000.tar.gz(r-4.6-any)
tidyestimate_1.1.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
tidyestimate/json (API)
NEWS

# 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:

Conda:

cancer-genomicstidy

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

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

TargetResultTimeFilesSyslog
linux-devel-x86_64OK135
source / vignettesOK174
linux-release-x86_64OK126
macos-release-arm64OK86
macos-oldrel-arm64OK104
windows-develOK102
windows-releaseOK100
windows-oldrelOK84
wasm-releaseOK109

Exports:estimate_scorefilter_common_genesplot_purity

Dependencies:clicpp11dplyrfarvergenericsggplot2ggrepelgluegtableisobandlabelinglifecyclemagrittrpillarpkgconfigR6RColorBrewerRcpprlangS7scalestibbletidyselectutf8vctrsviridisLitewithr

Using tidyestimate

Kai Aragaki

Rendered fromusing-tidyestimate.Rmdusingknitr::rmarkdownon May 28 2026.

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