Organisms and Galaxy package

[joachimwolff]

Hi,

Thanks for developing this great normalization technique!

I have two questions:

• Do you update the package concerning the available reference genomes? You offer mm9 and mm10, but we want to use the latest mm39.
• Have you written a Galaxy wrapper for CHIPIN?

Thanks and best,

Joachim

[valeu]

Dear Joachim,
thank you for your interest in our tool!
I did not know mm39 is already out. So, no, we don't have preprocessed files for this genome. I will ask the first author, Lelia, whether she can create them.
and we don't have a Galaxy wrapper, unfortunately..
Best wishes
Valentina

[joachimwolff]

Dear Valentina,

can you maybe just tell me how to create those files? I found a function for the exons ('create_exon') but not for the other files. Given those, we could recreate the files on our own.

Moreover, we tried to install the software as you describe, but it fails with:

── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/tmp/RtmpaImY3u/remotesa1b605ea61eb9/BoevaLab-CHIPIN-dcf5de9/DESCRIPTION’ ...
─  preparing ‘CHIPIN’:
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
         -----------------------------------
   ERROR: dependency ‘tiger’ is not available for package ‘CHIPIN’
─  removing ‘/tmp/RtmpwwiITo/Rinsta48d847b461ec/CHIPIN’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'CHIPIN' from GitHub:
  ! System command 'R' failed

We checked the tiger package, and it seems it was deleted. Can you provide a workaround for this?

Thanks and best,

Joachim

[LeliaP]

Dear Joachim,

I am Lélia Polit the first author of this package.
Concerning the issue with tiger please install the latest available version of it on your own (I used the version 0.2.3 available at https://cran.r-project.org/src/contrib/Archive/tiger/ )
I had to install ‘hexbin’, ‘qualV’, ‘klaR’, ‘som’ and ‘e1071’ to make it work on my side. Then if you face a problem with the package preprocessCore please use the biocmanager installation:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("preprocessCore")

For mm39 I will try to figure it out asap but if you want to do it on your own what is needed is:

• a file containing the sum of the exon lengths per gene that you can create using the function create_exons
• a bed file with the following columns: chromosome TSS_position TSS_position TSS_position gene_strand geneName
• a bed file containing the boundaries of the different genes: chromosome TSS TES geneName 0 gene_strand

Let me know if you do it otherwise I can create the files this week end.

Best
Lélia