Merge devel to master #435
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* biocbook: add GHA workflows * biocbook: move data to extdata * biocbook: move general/figures to inst/pages/images * biocbook: add vignettes * biocbook: add book assets * biocbook: update package files * biocbook: purge un-necessary files * biocbook: migrate Rmd to qmd and fix xrefs * biocbook: fix aesthetics * biocbook: add callout acknowledging miaverse in walcome page * biocbook: improve README to include dev/author instructions * biocbook: replace `js2264` by `microbiome` * Add section on network learning (#303) * Add section on network learning * Update section on network learning * Update network learning chapter Make requested changes Remove sections on network comparison * Add network comparison chapter * Update book.bib * Update chapters on network learning and comparison * biocbook: add `BiocBook` to `Suggests` for developers * biocbook: transfer chaps 60/61 to inst/pages/ --------- Co-authored-by: Stefanie Peschel <stefpeschel@gmail.com>
* Add section on network learning (#303) * Add section on network learning * Update section on network learning * Update network learning chapter Make requested changes Remove sections on network comparison * Add network comparison chapter * Update book.bib * Update chapters on network learning and comparison * Update network chapter and contributors (#377) - Reorder network learning chapter to be less nested - Move network plots to analysis section - Add contributors * #355: Add new data resource (#370) * #355: Add new data resource Signed-off-by: Daena Rys <rysdaena8@gmail.com> * Up Signed-off-by: Daena Rys <rysdaena8@gmail.com> * Up Signed-off-by: Daena Rys <rysdaena8@gmail.com> * Fix conflicts in book.bib Signed-off-by: Daena Rys <rysdaena8@gmail.com> --------- Signed-off-by: Daena Rys <rysdaena8@gmail.com> * Conversion to BiocBook (#379) * biocbook: add GHA workflows * biocbook: move data to extdata * biocbook: move general/figures to inst/pages/images * biocbook: add vignettes * biocbook: add book assets * biocbook: update package files * biocbook: purge un-necessary files * biocbook: migrate Rmd to qmd and fix xrefs * biocbook: fix aesthetics * biocbook: add callout acknowledging miaverse in walcome page * biocbook: improve README to include dev/author instructions * biocbook: replace `js2264` by `microbiome` * biocbook: add `BiocBook` to `Suggests` for developers * biocbook: transfer chaps 60/61 to inst/pages/ * biocbook: include changes from #370 and #377 --------- Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Stefanie Peschel <stefpeschel@gmail.com> Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com> Co-authored-by: Jacques Serizay <jacquesserizay@gmail.com>
Sync # Conflicts: # inst/assets/book.scss
* Merge devel to master (#432) * Conversion to BiocBook (#376) * biocbook: add GHA workflows * biocbook: move data to extdata * biocbook: move general/figures to inst/pages/images * biocbook: add vignettes * biocbook: add book assets * biocbook: update package files * biocbook: purge un-necessary files * biocbook: migrate Rmd to qmd and fix xrefs * biocbook: fix aesthetics * biocbook: add callout acknowledging miaverse in walcome page * biocbook: improve README to include dev/author instructions * biocbook: replace `js2264` by `microbiome` * Add section on network learning (#303) * Add section on network learning * Update section on network learning * Update network learning chapter Make requested changes Remove sections on network comparison * Add network comparison chapter * Update book.bib * Update chapters on network learning and comparison * biocbook: add `BiocBook` to `Suggests` for developers * biocbook: transfer chaps 60/61 to inst/pages/ --------- Co-authored-by: Stefanie Peschel <stefpeschel@gmail.com> * Revert "Conversion to BiocBook (#376)" (#378) This reverts commit ff3fdb3. * Master (#381) * Add section on network learning (#303) * Add section on network learning * Update section on network learning * Update network learning chapter Make requested changes Remove sections on network comparison * Add network comparison chapter * Update book.bib * Update chapters on network learning and comparison * Update network chapter and contributors (#377) - Reorder network learning chapter to be less nested - Move network plots to analysis section - Add contributors * #355: Add new data resource (#370) * #355: Add new data resource Signed-off-by: Daena Rys <rysdaena8@gmail.com> * Up Signed-off-by: Daena Rys <rysdaena8@gmail.com> * Up Signed-off-by: Daena Rys <rysdaena8@gmail.com> * Fix conflicts in book.bib Signed-off-by: Daena Rys <rysdaena8@gmail.com> --------- Signed-off-by: Daena Rys <rysdaena8@gmail.com> * Conversion to BiocBook (#379) * biocbook: add GHA workflows * biocbook: move data to extdata * biocbook: move general/figures to inst/pages/images * biocbook: add vignettes * biocbook: add book assets * biocbook: update package files * biocbook: purge un-necessary files * biocbook: migrate Rmd to qmd and fix xrefs * biocbook: fix aesthetics * biocbook: add callout acknowledging miaverse in walcome page * biocbook: improve README to include dev/author instructions * biocbook: replace `js2264` by `microbiome` * biocbook: add `BiocBook` to `Suggests` for developers * biocbook: transfer chaps 60/61 to inst/pages/ * biocbook: include changes from #370 and #377 --------- Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Stefanie Peschel <stefpeschel@gmail.com> Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com> Co-authored-by: Jacques Serizay <jacquesserizay@gmail.com> * Adding the troubleshoots notes for miaverse package installation based on [#368] (#409) * add instructions for Mac user installation * add troubleshoots installation Mac * fix indentation and long lines * add link to the troubleshoot file * spell check * spell check * Use mia from GH --------- Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Jacques Serizay <js2264@cam.ac.uk> Co-authored-by: Stefanie Peschel <stefpeschel@gmail.com> Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com> Co-authored-by: Jacques Serizay <jacquesserizay@gmail.com> Co-authored-by: erawijantari <45685102+erawijantari@users.noreply.github.com> * packages list updated and sorted * indentations updated --------- Signed-off-by: Daena Rys <rysdaena8@gmail.com> Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> Co-authored-by: Jacques Serizay <js2264@cam.ac.uk> Co-authored-by: Stefanie Peschel <stefpeschel@gmail.com> Co-authored-by: Leo Lahti <leo.lahti@iki.fi> Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com> Co-authored-by: Jacques Serizay <jacquesserizay@gmail.com> Co-authored-by: erawijantari <45685102+erawijantari@users.noreply.github.com>
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