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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tidyestimate.pdf |tidyestimate.html✨
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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:

cancer-genomicstidy

4.81 score 13 stars 4 scripts 309 downloads 3 exports 33 dependencies

Last updated 2 years agofrom:7f98f860d3. Checks:4 OK, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 01 2025
R-4.5-winOKFeb 01 2025
R-4.5-macOKFeb 01 2025
R-4.5-linuxOKFeb 01 2025
R-4.4-winNOTEFeb 01 2025
R-4.4-macNOTEFeb 01 2025
R-4.3-winNOTEFeb 01 2025
R-4.3-macNOTEFeb 01 2025

Exports:estimate_scorefilter_common_genesplot_purity

Dependencies:clicolorspacedplyrfansifarvergenericsggplot2ggrepelgluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcpprlangscalestibbletidyselectutf8vctrsviridisLitewithr

Using tidyestimate

Kai Aragaki

Rendered fromusing-tidyestimate.Rmdusingknitr::rmarkdownon Feb 01 2025.

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