cemordaunt / comethyl Goto Github PK

Hi Charles,

I was hoping to use comethyl on single cell WGBS methylome datasets (pseudo-bulked). Would that be a reasonable direction?

If so, can you please provide me example input files [an example of the Bismark Cytosine Reports and an example of sample_info.xlsx]?

We use an in-house pipeline to map the data and generate signal / count files called allC files which we describe here - https://hq-1.gitbook.io/mc/tech-background/file-formats#allc-file

Thanks,
Manoj.

Hi,

I attempted to install comethyl with the instructions given.

export R_LIBS=~/Rlibs
R

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> install.packages(c("BiocManager", "remotes"))

BiocManager::install("cemordaunt/comethyl")

ERROR: dependency ‘genefilter’ is not available for package ‘sva
ERROR: dependencies ‘GenomicFeatures’, ‘AnnotationDbi’ are not available for package ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
ERROR: dependencies ‘GenomicFeatures’, ‘AnnotationDbi’ are not available for package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
ERROR: dependencies ‘AnnotationDbi’, ‘AnnotationHub’, ‘GenomicFeatures’ are not available for package ‘annotatr’
ERROR: dependencies ‘GenomicFeatures’, ‘AnnotationDbi’ are not available for package ‘bumphunter’
ERROR: dependencies ‘GenomicFeatures’, ‘GO.db’, ‘AnnotationDbi’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘TxDb.Hsapiens.UCSC.hg38.knownGene’, ‘org.Hs.eg.db’ are not available for package ‘rGREAT’
ERROR: dependencies ‘bumphunter’, ‘annotatr’, ‘AnnotationHub’ are not available for package ‘dmrseq’

ERROR: dependencies ‘annotatr’, ‘biomaRt’, ‘dmrseq’, ‘GenomicFeatures’, ‘rGREAT’, ‘sva’, ‘WGCNA’ are not available for package ‘comethyl’

I edited this a bit, but it appears there are some missing dependencies that R doesn't know about where to install them from?

I tried using the install instructions for genefilter:

https://bioconductor.org/packages/release/bioc/html/genefilter.html

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

`ERROR: dependency ‘png’ is not available for package ‘KEGGREST’`

I was wondering if you were aware of these issues, or possible had any suggestions on resolving this? The host OS is rhel 7.7 (its a cluster head node.)

I was thinking I could try installing the various dependencies via spack, but there are an awful lot of them... anyhew. What OS is this working on? ubuntu? mac? Did I miss something obvious?