scialdonelab / mitohear Goto Github PK

Could you create the master branch as default, as now it goes to main which is empty?

https://github.com/ScialdoneLab/MitoHEAR

Also, would be great if you could add the license file.

P.S.
This is in reference to the JOSS review here:
openjournals/joss-reviews#4265

I like the Vignettes created with pkgdown (openjournals/joss-reviews#4265), but it's hidden in the README. Usually, the Vignettes URL is added to the description in the top right of the repo. It makes it more visible and gives a quick summary/overview of the package, especially when you search on GitHub. Below is how I do recommend it:

Yours show as:

We recommend including the URL and a few words about the package:

Again, this is not necessary but it's a good practice!

Thank you for all the changes you made to the repo (openjournals/joss-reviews#4265), I love the changes you made to the README .

Just a simple tip when adding code to the READEM - in order to increase the readability, we recommend highlighting the syntax by defining the language in code block ( e.g. ```r )

For example

current_wd <- getwd()
url <- "https://hmgubox2.helmholtz-muenchen.de/index.php/s/7P9C57RxfKnH5Qx/download/input_bam_files.tar.gz"
destfile <- paste0(current_wd, "input_bam_files.tar.gz")
download.file(url, destfile, quiet = FALSE)
untar(destfile, exdir=current_wd)

load(system.file("extdata", "after_qc.Rda", package = "MitoHEAR"))
cell_names <- as.vector(after_qc$new_name)
cell_names <- cell_names[1:5]
cell_names[1:5]
[1] "24538_8_14" "24538_8_23" "24538_8_39" "24538_8_40" "24538_8_47"

will be:

current_wd <- getwd()
url <- "https://hmgubox2.helmholtz-muenchen.de/index.php/s/7P9C57RxfKnH5Qx/download/input_bam_files.tar.gz"
destfile <- paste0(current_wd, "input_bam_files.tar.gz")
download.file(url, destfile, quiet = FALSE)
untar(destfile, exdir=current_wd)

load(system.file("extdata", "after_qc.Rda", package = "MitoHEAR"))
cell_names <- as.vector(after_qc$new_name)
cell_names <- cell_names[1:5]
cell_names[1:5]
[1] "24538_8_14" "24538_8_23" "24538_8_39" "24538_8_40" "24538_8_47"

by only adding r in the code block!

It is not necessarily added, but it makes the code more readable!

An example of some editing to the README file with a table of content can be seen in my fork here

Thank you again for your work!