Pinned issues
Issues
- 2
- 1
Episode 1: creating and subsetting vectors section has the wrong name of the `snps` variable.
#272 opened by naupaka - 1
Episode 3: convert your HTML images to markdown (but do not use the width parameter)
#270 opened by naupaka - 1
Add intro to MarkDown on Episode 01.
#203 opened by javibio-git - 0
In the exercise “Searching for R functions”, change “mixed linear model” to “linear model”.
#264 opened by naupaka - 0
After exercise “Searching for R functions”, add note that Google search is also a good way to get help for R functions.
#265 opened by naupaka - 0
Make the “save your script” instructions more prominent - maybe a warning box?
#261 opened by naupaka - 0
Add callout box explaining the difference between `==` and `%in%` at the end of “a few final vector tricks”
#258 opened by naupaka - 1
Consider unified setup page
#201 opened by ytakemon - 1
Tracking PR #91 : install R and RStudio locally
#199 opened by ytakemon - 0
Include instructions somewhere to Instructors to add learner names next to each instance in the spreadsheet. Learners need to only use the instance they are assigned.
#240 opened by naupaka - 1
- 0
CSV URL should be updated to point to the file within this repo (in main/data) instead of external user repo
#248 opened by naupaka - 2
Tracking PR #79 : Changing ggplot jitter use and adding boxplots + Travis CI issue
#198 opened by ytakemon - 0
inconsistent use of tidyverse in episodes
#237 opened by ggrimes - 18
Transition To Workbench in May
#204 opened by zkamvar - 0
ggplot2 sub-issue from beta test
#230 opened by ytakemon - 1
Grouped data
#224 opened by ggrimes - 3
Suggestion to update package cache
#217 opened by zkamvar - 0
Buoyant solution blocks in setup instructions
#220 opened by tobyhodges - 0
Link, Much of this lesson was copied or adapted from Jeff Hollister’s materials, broken
#212 opened by ggrimes - 6
Should this lesson should be labeled as beta?
#207 opened by sstevens2 - 1
Suggestions for improvements to the knitr lesson
#174 opened by vhmcck - 1
Links need to be fixed in CONTRIBUTING.md
#213 opened by tobyhodges - 1
All open PRs need to be merged or closed before May due to change over to Workbench infrastructure
#196 opened by naupaka - 1
Installing packages from Bioconductor vs from CRAN) seems pretty nuanced and advanced - is there a way to simplify this for the learner? I think we hadn't introduced installing from CRAN yet, before talking about Bioconductor?
#171 opened by naupaka - 5
Reports with knitr - consider recommending package tinytex for PDF reports
#194 opened by CarolynKoehn - 3
Merge into main, not into gh-pages
#191 opened by julianstanley - 2
First "tip" box is cutoff at a weird point
#190 opened by julianstanley - 1
Header level is off on “Second, install the vcfR package from Bioconductor using BiocManager”
#168 opened by naupaka - 1
Header level is off and broken screenshot on “Search for Bioconductor packages based on your analysis needs”
#169 opened by naupaka - 1
We haven’t talked about packages anywhere else, and only mentioned base R briefly. We may need a bit more material to introduce why packages are necessary/useful etc.
#170 opened by naupaka - 1
Installing packages from Bioconductor vs from CRAN) seems pretty nuanced and advanced - is there a way to simplify this for the learner? I think we hadn't introduced installing from CRAN yet, before talking about Bioconductor?
#173 opened by naupaka - 1
Remove the final “challenge” box on this page. Looks like an unfinished note to developers of things that are already incorporated into this episode.
#185 opened by naupaka - 1
Add a new challenge to this episode. Tracy had learners install a package of their choice from Bioconductor, but says “Feels risky to ask learners to install a package from the “wild” I’ve spent a fair amount of time running into trouble with dependencies, OS issues, etc.” Multiple learners had problems with installing packages, including some cases where our install of R wasn’t new enough.
#186 opened by naupaka - 2
Learner says that Package that we installed didn’t show up in our package list. Why is this and should we add a warning / callout about it?
#187 opened by naupaka - 1
Add a warning box about the long install process while vcfR is being installed due to many dependencies.
#188 opened by naupaka - 0
Make sure when learners are installing packages that we don’t have them install tidyverse - the server will hang. Just have them install the packages they need for the lesson - dplyr, tidyr, ggplot2.
#177 opened by ytakemon - 0
In “group by and summarize” section, take out the section using n() and go directly to tally(). Can then introduce summarize later with more complex examples.
#172 opened by ytakemon - 0
When installing packages at the start of the lesson, include tidyr. Otherwise have problems when trying to use pivot_wider or longer in this episode
#176 opened by ytakemon - 0
This challenge solution includes negation (!INDEL), which hasn’t been taught yet. Can instead do INDEL = FALSE
#165 opened by ytakemon - 0
Move explanation of QUAL from the mutate section to the first time QUAL is used (in challenge above).
#166 opened by ytakemon - 0
Change the code chunks in “creating and subsetting vectors” to use the snps vector instead of snp_genes. Currently, we have the learners create three new vectors and then not use them until 9 lines of code later.
#184 opened by poterlowicz-lab - 0
Some code chunks use single quotes for character vectors and some use double quotes. Make this consistent across all code chunks in lesson.
#183 opened by poterlowicz-lab - 0
In “a few final vector tricks”, note that NA stands for “not available”
#179 opened by poterlowicz-lab - 1
Review exercise 2 - missing line break
#182 opened by poterlowicz-lab - 0
Review exercise 1 - change `typeof()` to `mode()` to match what is taught earlier in lesson.
#180 opened by poterlowicz-lab - 1
For workshop admin team: When providing instance addresses for learners, include :8787 in the link so learners can click the link directly from the spreadsheet rather than copy/pasting into browser and adding :8787. Also make the spreadsheet READ ONLY for learners to prevent learners accidentally deleting AWS instances. Instructors will need write access to assign instances to individual learners.
#181 opened by JasonJWilliamsNY - 0
Missing line break in Exercise: Examining and subsetting vectors and in solution
#178 opened by poterlowicz-lab - 0
In “adding to, removing, or replacing values”, change `snp_genes[7]<- "APOA5"` to add in 6th position and remove note about NAs. NAs are introduced later in the episode.
#175 opened by poterlowicz-lab