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tidytof
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- Repository: https://github.com/keyes-timothy/tidytof
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Hi @keyes-timothy
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Type: Package
Package: tidytof
Title: Analyze High-dimensional Cytometry Data Using Tidy Data Principles
Version: 0.99.0
Authors@R:
c(person(given = "Timothy",
family = "Keyes",
role = c("cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-0423-9679")),
person(given = "Kara",
family = "Davis",
role = c("rth", "own"),
email = "[email protected]"),
person(given = "Garry",
family = "Nolan",
role = c("rth", "own"),
email = "[email protected]"))
Description: This package implements an interactive, scientific analysis
pipeline for high-dimensional cytometry data built using tidy data principles.
It is specifically designed to play well with both the tidyverse and
Bioconductor software ecosystems, with functionality for reading/writing
data files, data cleaning, preprocessing, clustering,
visualization, modeling, and other quality-of-life functions. tidytof
implements a "grammar" of high-dimensional cytometry data analysis.
License: MIT + file LICENSE
Depends:
R (>= 4.3)
Imports:
doParallel,
dplyr,
flowCore,
foreach,
ggplot2,
ggraph,
glmnet,
methods,
parallel,
purrr,
readr,
recipes,
rlang,
stringr,
survival,
tidygraph,
tidyr,
tidyselect,
yardstick,
Rcpp,
tibble,
stats,
utils,
RcppHNSW
Suggests:
ConsensusClusterPlus,
Biobase,
broom,
covr,
diffcyt,
emdist,
FlowSOM,
forcats,
ggrepel,
HDCytoData,
knitr,
markdown,
philentropy,
rmarkdown,
Rtsne,
statmod,
SummarizedExperiment,
testthat (>= 3.0.0),
lmerTest,
lme4,
ggridges,
spelling,
scattermore,
preprocessCore,
SingleCellExperiment,
Seurat,
SeuratObject,
embed,
rsample
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.1
LinkingTo:
Rcpp
URL: https://keyes-timothy.github.io/tidytof,
https://keyes-timothy.github.io/tidytof/
VignetteBuilder: knitr
Language: en-US
biocViews: SingleCell, FlowCytometry
(This is my first submission to Bioconductor - thank you for your help and patience in the review process! I'm sure I will learn a lot through this first experience.)
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidytof_0.99.0.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidytof to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Received a valid push on git.bioconductor.org; starting a build for commit id: 59311df58335792ec13076a2a913db09d6ebc5c9
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidytof_0.99.1.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidytof to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: b16165c8783c681995cd08f362e428df3aab9fe8
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidytof_0.99.2.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidytof to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: b2ea3cfa2377dd71fa59a30398817b2128349e5e
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidytof_0.99.3.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidytof to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 61551d4000427c17aa32241bab71277b0a3f9c57
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidytof_0.99.4.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidytof to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2f40d01f461bd9c25eeb3d5520672e1430f104c5
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidytof_0.99.5.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidytof to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 4fce362df3f0193b14f263a4788dc2ab0f711bf9
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidytof_0.99.6.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidytof to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thanks @keyes-timothy for this submission.
Given the amount of vignettes (11 in total), it's gonna be a challenge for a newcomer like me to navigate them:
There's a "Getting started with tidytof" vignette, so I suppose that users will be able to figure out where to start but then it's not clear where to go after that. Can the other vignettes be read in any order or is there an order that you recommend?
It would be nice if the introduction vignette could be made more prominent, maybe by using uppercase in the title (e.g. "GETTING STARTED with tidytof"), and if the introduction vignette had a "where to go next" section -- or something like that -- that lists the other vignettes in the recommended order of reading and provides a short description for each of them.
Also what does tof stand for? It's part of the package name and is the prefix of a bunch of function names defined in the package, but I can't figure out where it's comming from. I'm curious why you didn't choose tidycyto for the package name since it would have made the package's relationship with cytometry immediately obvious. Anyways would be nice to explain the tof acronym in the introduction vignette.
Thanks, H.
