Comments (5)
nilseling
commented on August 25, 2024
1
Alright, thanks for checking this. I have now updated the installation instructions in the README and started a cytomapper wiki with more detailed installation instructions.
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jwindhager
commented on August 25, 2024
Furthermore, for building the development version of cytomapper with vignettes, I needed to install:
sudo apt-get install libfontconfig1-dev
as well as the following R packages from CRAN:
install.packages(c("rmarkdown", "cowplot"))
and the following Bioconductor package:
BiocManager::install("BiocStyle")
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nilseling
commented on August 25, 2024
Hmm, for the R packages they should be installed by default since they are listed under Suggests. How did you install the cytomapper devel?
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jwindhager
commented on August 25, 2024
Maybe those are ignored by devtools::install_github?
Did the following, as indicated in the README:
devtools::install_github("BodenmillerGroup/cytomapper", build_vignettes = TRUE)
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nilseling
commented on August 25, 2024
Ok, I'll have a look. The build_vignettes parameter should trigger exactly this.
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Related Issues (20)
- Fix pattern argument in loadImages function HOT 1
- Keep metadata when compensating images HOT 1
- Make image handling more efficient HOT 11
- show clustering groups in cytomapper HOT 3
- Reader function for single-channel tiffs HOT 3
- CytomapperShiny gating only applies to one ROI of the 6 HOT 6
- mcols to colData HOT 2
- Strip out CytoImageList
- Cytomappershiny - Error: Graphics API version mismatch HOT 9
- Add option to remove cells after gating
- Developmental changes
- Setting custom breaks in colour parameter
- Bug in violin plot HOT 1
- Memory usage with big data sets HOT 3
- Color legend change
- Modifying `h5FilesPath` for `CytoImageList` object HOT 3
- Question for scale_bar for images used for publication? HOT 2
- Cytomappershiny questions HOT 2
- Fix corner case bug in cytomapperShiny
- In measureObjects, replace merge by left_join
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