Here's a few notes from the birds of a feather session at the Bioconductor Developer Day 2017-07-26

Writing papers in Rmarkdown, BiocStyle... (and books, posters)

Multi-panel figures

CRAN package multipanelfigure

Tables

knitr:  kable (ideally if you then also define your own CSS); xtable

interactive tables: DT CRAN package, an interface to JavaScript DT

see example in glimma

Titles and captions? pass to kable, and use HTML-style

tables package

Heatmaps

ComplexHeatmaps, pheatmap

Venn diagrams

upsetR

Caching  expensive computations or downloads

knitr ‘cache’ option for chunks     

BiocFileCache

Color palettes for figures

Rcolorbrewer; ggplot2 defaults; viridis, ggthemes, wesanderson, cardigans, dill/beyonce (github)

Convert from markdown to word:  pandoc

Bibliography styles for various journals:

rticles package:  by RStudio, and for their types of journals; community input for more styles? (should we care about proliferation of arcane citation ‘standards’?)

Authoring tutorials

http://swirlstats.com/

learnr package by J.J.

Posters

https://github.com/bbucior/drposter drposter

Books: bookdown

WIshlist:

Infinite scrolling, e.g. for reading on tablets

Track changes functionality?

For non-technical collaborators:

• How to annotate comments in the rendered PDF or HTML file and feed them back into the source: github?  There is a (are) JavaScript library(ies) that can annotate rendered HTML pages

• How to make changes on the rendered HTML and then feed them back?