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Bioconductor / OrchestratingSingleCellAnalysis

Content for the OSCA Book.
http://bioconductor.org/books/devel/OSCA/
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Figure 5.1 broken link #20

Closed johnomics closed 4 years ago

johnomics commented 4 years ago

Hello,

Thank you for writing such an excellent guide to single cell analysis.

Figure 5.1 is currently missing: https://osca.bioconductor.org/overview.html

The image is still in the repository: https://github.com/Bioconductor/OrchestratingSingleCellAnalysis/blob/master/images/Workflow.png

But the link appears to be incorrect, at line 46 of P2_W01.overview.md, which is then being propagated to line 676 of overview.html: https://github.com/Bioconductor/OrchestratingSingleCellAnalysis/blob/ed0b0930ab65a157fd5af8e8d4915adfb885cf70/docs/overview.html#L676

Please could you look into this? Thanks!

LTLA commented 4 years ago

Interesting. It seems like compiling a chapter with rmarkdown will embed an image into the HTML, but compiling with bookdown presumably just links to an image. Thanks for spotting this, given that the yet-to-be-compiled latest version of the book will encounter this problem for all of the external images. (Alas, my memes!)

johnomics commented 4 years ago

No problem - just noticed another even smaller bug too small for its own issue - Chapter 6 currently has two links to Section ??, because there is no quality-control-discarded anchor in P2_W02.quality-control.md.

LTLA commented 4 years ago

Oh, yeah, broken links are all over the place in that thing. I could get to them eventually, but you seem to be reading through the book anyway, so if you could list them (or even better, make a PR and fix them), that would be nice.

johnomics commented 4 years ago

Sure, I'll at least report them where I see them and fix them if I can. Thanks again for the great book.