Closed MartinFXP closed 5 years ago
Hi @MartinFXP
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:
Package: mnem
Type: Package
Title: mnem
Version: 0.99.0
Author: Martin Pirkl
Maintainer: Martin Pirkl <martin.pirkl@bsse.ethz.ch>
Description: Given a single cell populations from different perturbation experiments mnem infers sub populations with different states for a signaling pathway.
Depends: R (>= 3.4)
License: GPL-3
Encoding: UTF-8
LazyData: true
biocViews: Pathways, SystemsBiology, NetworkInference, Network, RNASeq, PooledScreens, SingleCell, CRISPR, ATACSeq, DNASeq
RoxygenNote: 6.0.1
Imports: cluster, nem, epiNEM, graph, Rgraphviz, flexclust, lattice, modeltools, naturalsort, snowfall, stats4, tsne, methods, graphics, grid, stats, utils
VignetteBuilder: knitr
Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit
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Received a valid push; starting a build. Commits are:
1f898a0 Deleted white space + version bump
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9fbb6f2 attended warnings and notes
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Received a valid push; starting a build. Commits are:
95d7163 reduced file size
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Received a valid push; starting a build. Commits are:
18c6a02 vignette bugfix
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Received a valid push; starting a build. Commits are:
17321b0 removed the devtools install and added bioconducto...
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Hi @MartinFXP,
Thanks for submitting the mnem package. Unfortunately it's almost impossible for me to use or review this package the way it's currently documented. The man pages and vignette are way too minimalist and cryptic. Please keep in mind that the purpose of contributing a package to Bioconductor is to share a tool that other people will be able to use.
Here are a few basic suggestions for improving the documentation and usability of the package:
Title of package should not be the same as its name.
Man pages have titles that are the same as description. The recommended practice is to use something different for the title and the description. The title is typically shorter and the description provides more details.
The app
dataset is a list of lists with a mysterious structure and content. The man page says "For details see the vignette" but AFAICT the vignette doesn't provide any detail about this data set. Please explain the structure and content of the data set. Also explain how it was generated.
The vignette contains too much code and almost no explanation about what the code is doing. The code seems to be generating many plots and graphs but these are not explained either.
Check for typos e.g. "genens" instead of "genes" or "finde" instead of "find" etc... There are many!
Try to find someone that has never used the package try to use it on its own data. S/he will provide very valuable feedback that will hopefully help you improve the usability of your package.
Thanks, H.
Received a valid push; starting a build. Commits are:
4afec7e extended help file descriptions and vignette minor...
Received a valid push; starting a build. Commits are:
ba669de forgot to include plot.bootmnem help file
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Received a valid push; starting a build. Commits are:
1a6e82e replaced last 1:... with seq_len
Received a valid push; starting a build. Commits are:
8ffd465 removed typo and added another
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Dear @hpages,
Thanks for the feedback. I addressed all of your concrete points accordingly and made the vignette more user friendly.
Title of package should not be the same as its name.
Fixed.
Man pages have titles that are the same as description. The recommended practice is to use something different for the title and the description. The title is typically shorter and the description provides more details.
Extended descriptions.
The app dataset is a list of lists with a mysterious structure and content. The man page says "For details see the vignette" but AFAICT the vignette doesn't provide any detail about this data set. Please explain the structure and content of the data set. Also explain how it was generated.
Explanation of the data object added to vignette.
The vignette contains too much code and almost no explanation about what the code is doing. The code seems to be generating many plots and graphs but these are not explained either.
I added echo=FALSE for code which is either for experts or just a derivation of shown code (i.e. only an index has to be changed to get the other plots).
Check for typos e.g. "genens" instead of "genes" or "finde" instead of "find" etc... There are many!
Ran spell check.
Best, Martin
Received a valid push; starting a build. Commits are:
da725a8 fixed bug which occurs at random probability initi...
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Received a valid push; starting a build. Commits are:
f0b6cf5 improved vignette
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Received a valid push; starting a build. Commits are:
1351aad DISC: weights work; responsibilities need some wor...
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Received a valid push; starting a build. Commits are:
b7ab083 full support for discrete/binary data (alpha tests...
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Received a valid push; starting a build. Commits are:
dec3376 added discrete example to vignette; improved table...
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Received a valid push; starting a build. Commits are:
bf98ad8 bump
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Received a valid push; starting a build. Commits are:
3aeab99 edit figure captions; sim data explanation
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Received a valid push; starting a build. Commits are:
d9789d6 removed typos; added nem references
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f3cacdd updated citation; added multi knockout support; bu...
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a95cc16 back to R >= 3.5
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Received a valid push; starting a build. Commits are:
8f08398 minor corrections to get the buzzards off my back
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