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DEXSeq: How to reduce compute time for estimating dispersions for large datasets.
dexseq estimatedispersions large dataset
2.8 years ago mjrarcher ▴ 10
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Why does DEseq2 take a long time to run on large dataset ?
DEseq2 large dataset
updated 2.9 years ago by 34k • written 2.9 years ago by ▴ 10
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Eliminating repetitive calls to ExperimentHub
experimenthub annotationhub large dataset
3.4 years ago slinker ▴ 20
3 results • Page 1 of 1
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Comment: Interpretation of Log 2 fold change by adeler001 • 0
Thank you much James
Answer: Getting Bioconductor genome wide annotation for Candida auris by James W. MacDonald 58k
There isn't an `OrgDb` for C. auris on the `AnnotationHub`, so you will need to generate one yourself, using `makeOrgPackageFromNCBI` in th…
Comment: Getting Bioconductor genome wide annotation for Candida auris by Javan Okendo • 0
@James I am using clusterProfiler: https://learn.gencore.bio.nyu.edu/rna-seq-analysis/gene-set-enrichment-analysis/ for the enrichment anal…
Comment: Error: package or namespace load failed for ‘clusterProfiler’: object ‘get_fun_f by Chan • 0
Hi, I'm having a same problem with the 4.0.3 version of R. How did you download the older version 0.1.3 of rvcheck? I tried multiple ways.
Comment: Getting Bioconductor genome wide annotation for Candida auris by James W. MacDonald 58k
You have tagged `AnnotationHub` in your question, so I presume you know about that. Is there no C. auris data available? Also, what do you …
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Comment: Getting Bioconductor genome wide annotation for Candida auris
Answer: Getting Bioconductor genome wide annotation for Candida auris
Answer: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE
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