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rmarkdown
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reset
3
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3
replies
16k
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Error in Knit R Markdown document (could not find function "Biocexptpkg")
rmarkdown
rstudio
knitr
8.1 years ago
Jon Bråte
▴ 260
0
votes
2
replies
3.9k
views
Error in file.choose() : file choice cancelled
package development
bioconductor
rstudio
rmarkdown
vignettes
7.0 years ago
clarisbaby
• 0
0
votes
2
replies
3.6k
views
installation of package 'rmarkdown' had non-zero exit status
rmarkdown
package updates
updated 8.2 years ago by
James W. MacDonald
67k • written 8.2 years ago by
tarek.mohamed
▴ 10
6
votes
1
reply
3.5k
views
Tutorial:
BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
biocstyle
Rmarkdown
Tutorial
7.3 years ago
Wolfgang Huber
★ 13k
10
votes
3
replies
3.4k
views
News:
Updates to BiocStyle formatting
BiocStyle
vignettes
rmarkdown
latex
News
7.2 years ago
Andrzej Oleś
▴ 750
5
votes
3
replies
2.4k
views
Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chunk
rmarkdown
suppressWarning
warning
updated 20 months ago by
Mike Smith
★ 6.6k • written 2.9 years ago by
Wolfgang Huber
★ 13k
3
votes
2
replies
1.9k
views
Issue with pandoc-citeproc when rendering the f1000 article Rmd file from BiocWorkFlowTools
BiocWorkflowTools
rmarkdown
updated 7.4 years ago by
Andrzej Oleś
▴ 750 • written 7.4 years ago by
Leonardo Collado Torres
★ 1.1k
1
vote
2
replies
1.6k
views
Display BrowseSeqs output in R Notebook?
BrowseSeqs
DECIPHER
notebook
rmarkdown
updated 5.2 years ago by
Erik Wright
▴ 150 • written 5.2 years ago by
lauren.fitch
• 0
1
vote
1
reply
1.3k
views
Having issues mapping gene Ids during ReportingTools::publish() from Bioconductor.
ReportingTools
RNA-Seq
RMarkdown
updated 4.2 years ago by
James W. MacDonald
67k • written 4.2 years ago by
anthony.nash
▴ 20
1
vote
1
reply
1.3k
views
Best practices for sharing RMarkdown-based supplemental PDFs?
rmarkdown
knitr
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Keith Hughitt
▴ 180
0
votes
0
replies
734
views
Author footnotes in BiocWorkflowTools::f1000_article template
BiocWorkflowTools
rmarkdown
4.4 years ago
helucro
▴ 70
11 results • Page
1 of 1
Recent ...
Replies
Answer: single cell RNA seq pseudobulk batch correction
by
James W. MacDonald
67k
You can exclude the females from the non-responders.
Answer: Normalized counts to be used in decoupleR from deseq2 results
by
James W. MacDonald
67k
No, you never use normalized counts for anything but plotting. Can you point out the example that uses normalized counts?
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
If you care to know more about the process, there is a [GitHub with all the code][1]. It's pretty complicated though - the readme alone is …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Guido Hooiveld
★ 4.1k
Thanks; I did not know which file exactly is being used. Good catch regarding the discrepancy between the 2 web pages. I will get in touch …
Answer: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
The data for the `OrgDb` packages comes directly from NCBI, and in this case the symbols come from the gene_info.gz file you [can get from …
Votes
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
Comment: limma technical repeat correction
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