bioconductor / biocworkshops

:warning: 2018 :warning: Bioconductor Workshops

knit	title	description	site	github-repo	documentclass
bookdown::render_book	The Bioconductor 2018 Workshop Compilation	This book is a central repository for all the workshops submitted to the Bioconductor 2018 Conference	bookdown::bookdown_site	Bioconductor/BiocWorkshops	book

This work is licensed under a Creative Commons Attribution 4.0 International License.

The most up-to-date error messages and .md files from builds of individual workshops are here.

Introduction

Author: Martin Morgan^[Roswell Park Comprehensive Cancer Center, Buffalo, NY].
Last modified: 22 May, 2018.

The most recently compiled version of the book is available at https://bioconductor.github.io/BiocWorkshops/.

For Everyone

This book contains workshops used in R / Bioconductor training. The workshops are divided into 3 sections:

• Learn (100-series chapters) contains material for beginning users of R and Bioconductor. The Bioconductor-related material is relevant even for experienced R users who are new to Bioconductor.

• Use (200-series chapters) contains workshops emphasizing use of Bioconductor for common tasks, e.g., bulk RNA-seq differential expression, ChIP-seq, single-cell analysis, gene set enrichment, and annotation.

• Develop (500-series chapters) contains workshops to help expert users hone their skills and contribute their domain-specific knowledge to the Bioconductor community.

For Workshop Authors

To contribute a new workshop, open a BiocWorkshops issue asking to be added as a collaborator.

DESCRIPTION

Update the DESCRIPTION file adding packages utilized in your workshop to the Imports field. Please be kind and don't remove anyone elses packages from the DESCRIPTION as this is a shared file for all workshops. Also don't add your packages to the Depends field.

Classifying your workshop

Follow the numbering scheme above to classify your workshop by preceding your title with "Bioconductor 1xx:", "Bioconductor 2xx:", or "Bioconductor 5xx:". Final workshop numbers will be determined by an editor.

Bookdown

Write your workshop as a stand-alone markdown document, using your workshop syllabus already posted here as a starting point. We are using bookdown ('knit-then-merge' strategy) to compile the workshops and produce a book that will be available through Continuous Integration at https://bioconductor.github.io/BiocWorkshops/.

You do not need to build the complete book yourself, it is sufficient to ensure that your own workshop compiles successfully. You can 1) compile draft versions using a standard "knit" procedure to compile your chapter, and 2) follow these bookdown procedures to see how your chapter will look in the finished product. Install the bookdown package package from CRAN, as well as pandoc. Render your chapter with the preview= option to render_book(), e.g.,

Rscript -e "bookdown::render_book(                             \
    'xxx_Your_Workshop.Rmd', 'bookdown::gitbook', preview=TRUE \
)"

As this is a shared space for all workshop contributors, in order to use the above command in the BiocWorkshops directory, the index has to be built at least once, which can be time consuming depending on how many workshops have already been submitted.

Rscript -e "bookdown::render_book(                             \
    'index.Rmd', 'bookdown::gitbook')"

To avoid having to build all workshops but still be able to preview your individual workshop we recommend creating a soft link to your .Rmd file. We recommend having the file in the BiocWorkshop/ and the soft link in any other directory on your system. By default, this will generate an html file in _book/ wherever this command is run.

mkdir tmp
cd tmp/
ln -s ../xxx_Your_Workshop.Rmd
Rscript -e "bookdown::render_book(                             \
    'xxx_Your_Workshop.Rmd', 'bookdown::gitbook', preview=TRUE \
)"

Push only your .Rmd file to the BiocWorkshop repository; the book will be rebuilt manually or automatically. Eventually the output will be available for end-users at https://bioconductor.github.io/BiocWorkshops .The master branch will not contain the built version of the book. Switching to the gh-pages branch will show built output.

Deadlines for Bioc2018

Please be aware of the following deadlines for the Bioconductor 2018 Conference in Toronto

• Fri June 29: draft workshop materials submitted to this Bioconductor GitHub bookdown site

• Fri July 6: feedback period completes

• Weds July 18: workshops must pass checks without errors or warnings (All materials will be checked by Continuous Integration)

• Thurs / Fri July 26-27: Bioc2018

biocworkshops's Issues

Lawrence_GenomicRanges.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

PDF of 500_Effectively_Using_the_DelayedArray_Framework.Rmd

Loading required package: ggplot2
Quitting from lines 225-330 (500_Effectively_Using_the_DelayedArray_Framework.Rmd)
Error in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  invalid font type
Calls: local ... drawDetails -> drawDetails.text -> grid.Call.graphics
In addition: There were 19 warnings (use warnings() to see them)

Execution halted
Error in Rscript_render(f, render_args, render_meta) :
  Failed to compile 500_Effectively_Using_the_DelayedArray_Framework.Rmd
Calls: <Anonymous> ... render_new_session -> tryCatch -> tryCatchList -> Rscript_render
Execution halted

When building on the AMI.

Added as collaborator for workshop

Hi,

I'm following the instructions to be added as a collaborator for my workshop.

Please add me as a contributor

230_Isserlin_RCy3_intro.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

ERROR: cytoscapeVersionInfo not found DUPLICATE

text and figures run off page in PDF version

e.g. see page 48 (Annotation lab, R output), 242/243/245/249/251 (Cytoscape lab, imported graphics)

201_Love_DESeq2.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note any problems and status updates here.

Turaga_MaintainBioc.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

Per-chapter references?

Right now, it appears that the references are all getting added to the last chapter. A quick check turned up this post:

https://stackoverflow.com/a/48198032/459633

Can we try that to see if we end up with per-chapter bibliographies?

Please add me as collaborator

500_Effectively_Using_the_DelayedArray_Framework.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

ERROR: can't open file @line 559

Citations

It looks like we can maintain separate bib files, and list them all together when merging Rmd.

https://bookdown.org/yihui/bookdown/citations.html

Does this sound correct?

I would then maintain something like 201_Love_DESeq2.bib and I could have a dummy tmp/index.Rmd to store the bibliography-specifying chunk of YAML while I'm working?

Publish book on bookdown.org?

After the conference could also put the book on https://bookdown.org/? Might be a good way to promote Bioc to other R users.

Please add me as a collaborator

Thanks!

Bookdown PDF

Gives a 404:

https://bioconductor.github.io/BiocWorkshops/BioC2018.pdf

Please add me as a collaborator

Ramos_MultiAssayExperiment.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

Waldron_PublicData.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

Where and how to classify workshops within the respective RMD file?

Quoting from the README:

• Use (200-series chapters) contains workshops emphasizing use of Bioconductor for common tasks
• Follow the numbering scheme for classifying your workshop

Where and how am I supposed to annotate that within my RMD file?

Within the header or as a subheading?

220_Das_SingleCellRNASeq.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

aroma.light issue, to be resolved on server side.

Please add me as collaborator

New collaborator for workshop: functional enrichment analysis (Geistlinger)

Please add me as a collaborator for the workshop Functional enrichment analysis of high-throughput omics data. Thanks!

Please add me as a collaborator.

100_Morgan_RBiocForAll

This workshop is a little under the radar and wasn't listed as an issue or on the projects page, so I'm posting this to let the organizers know that the workshop is complete as a draft.

Cooley_DECIPHER.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

Workshop is currently incomplete

Coetzee_StatePaintR.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

230_Isserlin_RCy3_intro.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

ERROR: cytoscapeVersionInfo not found

Incomplete or Erroring Workshops

Dear Workshop Contributors,
@mikelove @lwaldron @PeteHaitch @risserlin
@sa-lee @drisso @zhaleh-safikhani @kstreet13
@lgeistlinger @npcooley @Simon-Coetzee @nturaga
@vobencha

A few items are still unresolved for getting a complete workshop build.

• Please check the _bookdown.yml file and the assigned issue for the status of your workshop
• Make sure that you are using the appropriate Rmd file for your workshop (there should be no duplicate workshop files)
• Ensure that you are modifying the DESCRIPTION file and your package list accordingly so that all dependencies are documented

Best regards,
Marcel

cc: @mtmorgan @lshep

Geistlinger_Omics.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

affected by aroma.light installation issue, will be resolved on server side.

Including data from a non-Bioc package

I have data from a previous tutorial in a package available through GitHub but not Bioc. Can we somehow integrate that using devtools or something?

Safikhani_Pharmacogenomics.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

Parallel builds--idea for next year

For next year, it would be useful to develop a parallel build strategy to use multicore where possible and minimize rebuilds when not needed. Knitr caching helps, but particularly when running in an environment where the underlying code and R are not changing, remaking .md from .Rmd is wasteful.

Please add me as a collaborator

Thanks,
Stuart

RCy3 connection issues from amazon instance

Rcy3 communicates with cytoscape using the localhost on the machine that is running Rstudio but the amazon instance is not able to access localhost calls.

I think that what is suggested in this post (https://stackoverflow.com/questions/43488046/cant-connect-to-localhost-apache-ubuntu) might work but I got permission denied error when I tried.

Can we enable ssh connection to the amazon instances so people can try the Rcy3 calls from amazon instance.

Instructions for using the materials

@seandavi @lshep can you update the index.Rmd file where I put in your names with instructions for setting yourself up to use the materials?

Lee_Plyranges.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

error use dplyr::filter

Using package hosted on github for helper code

I wanted to follow up on the the discussion from issue #16. For the pharmacogenomics ML workshop, @zhaleh-safikhani developed a package with some helper code that does things such as running Cross Validation and plotting the ML results. The package is hosted on github at bhklab/PharmacoGxML. We don't have plans to make this package available on BioC, since its just the helper functions for the workshop.

The question we wanted to is how important it is to keep the markdown document as a self-contained file? There are a handful of largely uninteresting function definitions in that package, which we could in theory include in the markdown to make a self contained document and remove the dependency. However, the large blocks of code distract from the legibility and content in our opinion. If I interpret @zhaleh-safikhani's intent correctly, the idea behind the workshop isn't necessarily to describe basic machine learning concepts, but to point out the challenges in applying them to these pharmacogenomic data types and how to get started with your analysis in this field.

We also depend on another package (bhklab/mCI) we are hoping to push out soon for a method recently developed in the lab, but its also currently only on github. Is there anything we need to do except edit the Imports and Remotes fields of the description for the document to build?

Please add me as a collaborator

risserlin

Please add me as a collaborator

Thank you

Law_RNAseq123.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

Including non-package example data

I've a small (3 kb) HDF5 file I'd like to include as part of my workshop.
Is this permitted?
If so, should I follow something like #12 (comment)?

Use of png images

Hi,

in last year's workshop, we started our Rmd file with a schema of a typical single-cell workflow, which we included simply by using

knitr::include_graphics("schema_workflow.png")

That means including a (small) png file to the repository. Is that OK, or is it discouraged?

please add me as a collaborator

thanks!

Licensing of all material

I don't think we have an agreed-upon license. Having such a thing in place and having contributor signoff for that license is probably worth doing after the dust settles from the conference.

Add Google Analytics tracking

See here, for example:
https://benmarwick.github.io/bookdown-ort/mods.html#google-analytics

Please add me as a collaborator

For submitting my workshop for BioC2018.
Thanks!

Using a single chapter?

How can I use a single chapter, e.g., the 100 series introduction? By 'use' I mean both tell my audience 'do XXX' (git clone would be acceptable, but not cloning the whole book) and also for me tweaking the material for a particular presentation (e.g., removing the intro to R section of the 100 workshop).

My hack was to copy the file & supporting material to a new git repository, but of course now I've got two slightly different versions and some extra work to merge changes back.

Continuous Integration

@LiNk-NY I think this line should be like the example in index.Rmd, where the first argument is the name of the Rmd file in the git commit that triggers the build, and where the third argument is TRUE -- this will then just build the workshop that is being committed, rather than the entire collection of workshops; building the entire collection will become expensive.

MacDonald_Annotation.Rmd

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

Citations not displayed properly

I noticed this on my workshop, and @mikelove's and @drisso's workshops that references aren't being displayed properly.

For example:
https://bioconductor.github.io/BiocWorkshops/rna-seq-data-analysis-with-deseq2.html#preparing-data-for-deseq2
The citation key is being shown rather than author and year.

I thought I would've got around this by specifying a bibliography argument in the yaml at the top of my Rmd but maybe that gets ignored when buidling the entire book. Maybe the bib files should be placed in _output.yml?