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Home Page: http://bioconnector.github.io/workshops
License: Other
Bioconnector Workshops
Home Page: http://bioconnector.github.io/workshops
License: Other
the rmarkdown lesson links to some out of date resources. e.g., https://github.com/bioconnector/workshops/blame/252121cfaa059c318d75778512c2e1f81d6e26ce/r-rmarkdown.Rmd#L27. probably should clean these up. cc @vpnagraj (you're teaching this one right @vpnagraj?)
index.md/html is pretty boring, and mostly leftover cruft from bims8382. update this to make it more relevant to the workshop series, perhaps with links to registration on the dot edu site.
topics page in navbar mostly pertains to leftovers from BIMS8382. this should go away, or be rolled into the lessons menu, or perhaps moved into an existing page under the ? menu
BIMS8382 class 2016 was made by using a Makefile to render all Rmd files to HTML, and committing all files to both master and gh-pages (source. Using RMarkdown websites has been much easier to maintain here, and cleaner (only source files on master, only rendered files on gh-pages).
Rather than going back and updating bioconnector/bims8382, I'd like to use Rmarkdown website functionality for rendering the 2017 course materials. Instead of going back to bioconnector/bims8382 and updating everything, and maintaining two parallel repos, I propose we add bims8382-specific materials to this repo. Do you agree, @vpnagraj ?
Some things to do (check them off here as you create separate issues):
the kubrik table here http://bioconnector.org/workshops/r-interactive-viz.html#highcharter doesn't print nicely, too wide. consider selecting out a few columns?
the survival analysis lesson states that you should use the death data, but filters where etype==1 (recurrence, not survival). options are:
etype==1
to 2
and update all output and exercises.2 is probably a better option.
Keep an eye on https://github.com/hadley/precis - maybe useful for replacing base::summary() for data frames especially if it becomes a canonical part of the tidyverse.
add pdf exercises to handouts
Add exercises for stats lesson
add commands to install all packages needed to build the site.
Better in the README or CONTRIBUTING md file? @vpnagraj
may obviate the need for the git deploy subtree madness
https://github.com/blog/2228-simpler-github-pages-publishing
stats lesson problem ex 2 doesn't specify outcome variable
40b85aa added results from IPA on significant results. add some of these to the end of the RNA-seq lesson.
Handout should have background section with information about the cox model, and knitted exercises.
"good enough..." is published:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510
see also: COS, Leek, more recent papers...
Nice list from Mike Love
Rendered: https://biodatascience.github.io/compbio/
Source: https://raw.githubusercontent.com/biodatascience/compbio/gh-pages/index.Rmd
The RNA-seq lesson really needs to be updated to the latest best practices starting with transcript quantification rather than alignment and gene-counting. Rough outline:
student had trouble installing tidyverse on 3.1.0. looks like tibble requires >=3.1.2. Perhaps require >=3.2.0?
http://www.sthda.com/english/wiki/survminer-0-2-4
Of note: surv_summary()
, faceting ggsurvplot()
, and using ggsurvplot()
to plot a cox model. Also new functions for visualizing optimal cutpoints. See post above for details, and update lesson.
add a contributing file that links to resources used to build this using the rmarkdown website framework. also, document how to push _site to gh-pages using a subtree push. add this file to the exclusion list on _site.yml, e.g.,
exclude: ["contributing.md"]
Thanks for all your contribution. The website is wonderful, I can learn a lot.
Some warnings on building the interactive viz lesson:
Warning messages:
1: 'hc_add_series_scatter' is deprecated.
Use 'hc_add_series' instead.
See help("Deprecated")
2: 'hc_add_series_scatter' is deprecated.
Use 'hc_add_series' instead.
See help("Deprecated")
Line 216 in the ncbi lesson fails...
entrez_fetch(db = "nuccore", id = nuclinkid, rettype = "fasta")
...with the error:
Error in curl::curl_fetch_memory(url, handle = handle) :
Operation was aborted by an application callback
This results in a build error. In 1022146 I turned off (eval=FALSE
) a few chunks that create or refer to this data.
I get the following warnings when I build:
Output created: docs/index.html
Warning messages:
1: package 'DESeq2' was built under R version 3.3.1
2: package 'S4Vectors' was built under R version 3.3.1
3: package 'GenomeInfoDb' was built under R version 3.3.1
4: Removed 32155 rows containing missing values (geom_point).
5: Removed 32270 rows containing missing values (geom_point).
Some of these should be required/recommended reading for particular workshops:
add to stats lessons:
dplyr 0.5 and tibble 1.1 introduce some breaking changes. things that come to mind are
perhaps @vpnagraj could help test this one and suggest changes
Output created: _site/index.html
There were 12 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: Removed 166 rows containing non-finite values (stat_bin).
2: Removed 31 rows containing non-finite values (stat_bin).
3: Removed 31 rows containing non-finite values (stat_bin).
4: Removed 166 rows containing missing values (geom_point).
5: Removed 31 rows containing non-finite values (stat_smooth).
6: Removed 31 rows containing missing values (geom_point).
7: Removed 723 rows containing non-finite values (stat_bin).
8: Removed 31 rows containing non-finite values (stat_boxplot).
9: Removed 31 rows containing non-finite values (stat_smooth).
10: Removed 31 rows containing missing values (geom_point).
11: Removed 31 rows containing non-finite values (stat_smooth).
12: Removed 31 rows containing missing values (geom_point).
options:
na.omit
before plotting.keep_all = TRUE
See http://dplyr.tidyverse.org/news/index.html#dplyr-0-5-0-9000
as_tibble()
will soon be exported from tibble in dplyr, and tbl_df()
will be deprecated.
from 2014-2015, add link on homepage or FAQ page somewhere.
https://twitter.com/hadleywickham/status/773264703711617024
The tidyverse package installs and loads pretty much all the tidy packages we use here - ggplot2, dplyr, readr, tidyr, tibble, stringr, broom, etc.
Once this hits CRAN (next week?) change setup instructions and lesson-specific library
calls.
The following lines seems to be causing a build failure.
recs <- entrez_fetch(db = "pubmed", id = res$ids[1:25], rettype = "xml", parsed = TRUE)
recs <- entrez_fetch(db = "pubmed", web_history = res$web_history, rettype = "xml", parsed = TRUE)
They both work fine when run interactively but throw the following error when trying to knit the Rmd.
Error in entrez_check(response) :
HTTP failure: 502, bad gateway. This error code is often returned when trying to download many records in a single request. Try using web history as described in the rentrez tutorial
Calls: <Anonymous> ... entrez_fetch -> do.call -> <Anonymous> -> entrez_check
Execution halted
Exited with status 1.
I turned these off with eval=FALSE
for now.
http://bioconnector.org/workshops/r-rmarkdown.html
https://github.com/bioconnector/workshops/blob/master/r-rmarkdown.Rmd
This whole lesson probably needs reworking. No one needs to know the gory details presented here. It should really be taught top-down instead of bottom up. Show people some RMarkdown in action first, then get into the details.
See also #49 - the reproducible research section is woefully out of date.
Some resources to look at:
On reproducibility:
Reproducibility and replicability is a glossy science now so watch out for the hype · Simply Statistics
https://simplystatistics.org/2017/03/02/rr-glossy/
Instead of research on reproducibility, just do reproducible research · Simply Statistics
https://simplystatistics.org/2015/12/11/instead-of-research-on-reproducibility-just-do-reproducible-research/
A Simple Explanation for the Replication Crisis in Science · Simply Statistics
https://simplystatistics.org/2016/08/24/replication-crisis/
Practical computational reproducibility in the life sciences | bioRxiv
https://www.biorxiv.org/content/early/2017/10/11/200683
Project-oriented workflow - Tidyverse
https://www.tidyverse.org/articles/2017/12/workflow-vs-script/
cc @vpnagraj
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