montilab / bs831 Goto Github PK

We should add the license document, especially since this is publicly available.

We need to clean up the installR.R script to include the bare minimum set of packages, so as to minimize possible installation failures.

Can we adopt the output format used for shine? The style is much nicer.

Warning: object ‘dm10’ is created by more than one data call

I updated into R4.2.3 and trying to install BS831 package as instructed, but obtained error message below.

devtools::install_github("montilab/BS831")
Downloading GitHub repo montilab/BS831@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/montilab/BS831/tarball/HEAD' failed

Add example of bidirectional signature (with both left- and right-skewed hits).
Useful to explain the computation of the GSVA score with mx.diff=TRUE.

** byte-compile and prepare package for lazy loading
Error in get(genname, envir = envir) : object 'testthat_print' not found

If you look at vignettes/docs/DiffanalysisRNAseqComparison.Rmd, at the very end, you'll see that the counts for the two visualizers differ. In particular, the overlap between limma and DESeq2 is 343 (venn.diagram) vs. 218 (vennr).

Hi, BS831 is really nice resource for learning, however, I am not writing this for an issue, but I like to know how to determine the features that contribute most towards the cluster during clustering using ConsensusClusterPlus (or for that matter any clustering algorithm)?

I have a dataset with 928 rows * 473 columns (sample), but when I looked at the consensus matrix, the dimension does not match (matrix dim ~ 473 * 473). I know this is not your package, but I hope I could get some hints on how to address this issue.

Best,

Need to fix:
WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘BS831/data/TCGA.BRCA25.rda’
─ building ‘BS831_1.20.0.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘BS831/docs/articles/docs/DiffanalysisRNAseqComparison_files/accessible-code-block-0.0.1/empty-anchor.js’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘BS831/docs/articles/docs/Dimensionality_Reduction_files/plotly-htmlwidgets-css-1.52.2/plotly-htmlwidgets.css’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘BS831/docs/articles/docs/GeneSetProjectionASSIGN_files/figure-html/plot assign scores and gene expression-1.png’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘BS831/docs/articles/docs/GeneSetProjectionASSIGN_files/figure-html/plot assign scores and gene expression-2.png’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘BS831/docs/articles/docs/GeneSetProjectionASSIGN_files/figure-html/plot assign scores and gene expression-3.png’

Need to add (possibly floating) Table of Contents to the Mardkdowns at github.io.
The TOC appears in some module, but not in others, although they all have the same 'preamble'.
See, e.g., DiffanalysisRNAseqComparison.Rmd (doesn't appear) vs. RNAseq_ScalNorm.Rmd (appears)

I like better the original name, more general and descriptive. And I would like to think of this as a useful repository beyond BS831