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Maria Doyle
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shepherl
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9 months ago
info
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shepherl
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shepherl
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11 months ago
Maria Doyle
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Gene Set Enrichment Analysis in Bioconductor course
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11 months ago
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11 months ago
Maria Doyle
▴ 110
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Mass Spectrometry and Proteomics with R/Bioconductor course
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12 months ago
info
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329
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12 months ago
Maria Doyle
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12 months ago
Maria Doyle
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585
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12 months ago
info
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4
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Maria Doyle
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15 months ago
shepherl
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467
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15 months ago
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15 months ago
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23 months ago • updated 15 months ago
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15 months ago
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News:
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Release
updated 8 months ago by
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• 0 • written 16 months ago by
shepherl
4.3k
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610
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News:
Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment
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15 months ago
info
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667
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News:
RNAseq data analysis with Bioconductor (online course)
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15 months ago
info
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916
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News:
Subject: Last 2 Seats Available for Metabolomics with R/Bioconductor Course (October 7-10)
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updated 16 months ago by
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16 months ago
Maria Doyle
▴ 110
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772
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News:
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16 months ago
info
▴ 10
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Answer: Confirm that OpenStats will not be archived (pryr dependency)
by
shepherl
4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Michael Love
43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Federico Marini
▴ 180
Jumping in on this - all this started because we want to "do it right", i.e. avoiding the post-hoc filtering on the logFC (which is still w…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Michael Love
43k
it looks above like you have a gene with two non-zero count samples. Also, yes you can use a stricter filter. You cannot estimate the LFC …
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq
by
Ahmed Salah
• 0
Thank you very much for your answer. Actually, this is after pre-filtering ```r keep <- rowSums(counts(dds) >= 10) >= 3 dds <- dds[keep, …
Votes
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
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