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A way to find which genome builds a package supports
build
genome
13 months ago
Dmitry
• 0
0
votes
1
reply
710
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Error in the Multiple platform build/check report for BioC 3.15
build
BuildReport
updated 2.3 years ago by
Mike Smith
★ 6.5k • written 2.3 years ago by
Meriem
• 0
1
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1
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455
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Mac/Windows test build systems?
build
updated 2.5 years ago by
shepherl
3.8k • written 2.5 years ago by
hstern2
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News:
Release Deadline: Passing R CMD build and R CMD check
package
build
build/check error
check
release
News
6.1 years ago
shepherl
3.8k
1
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3
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1.5k
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How to access error log from build report
build
testthat
cmd check
updated 8.5 years ago by
James W. MacDonald
65k • written 8.5 years ago by
Peter
• 0
2
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3
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1.2k
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Building a reduced BSgenome.Gallus.UCSC.galGal 4 from Bioconductor
r
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genome
chicken-sheme
8.5 years ago
pertille
• 0
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Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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