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News: Reminder: BioC2023 in-person registration closes 19th July!
Bioconductor BioC2023 Conference
11 weeks ago Maria Doyle ▴ 30
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News: May 31st is the last day to nominate for Bioc2023 Awards!
Bioconductor Awards Bioc2023 Recognition
4 months ago shepherl 3.5k
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News: Reminder: BioC2023, Awards, TAB Deadline approaching - May 31st!
Bioconductor Community BioC2023
4 months ago Maria Doyle ▴ 30
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News: Last Week to Nominate for Bioc2023 Awards!
Bioconductor Bioc2023 Recognition Awards
4 months ago shepherl 3.5k
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News: Junior Developer or New Package Developer Award
Bioconductor Recognition Bioc2023 Awards
4 months ago shepherl 3.5k
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News: Bioconductor Community Engagement, Outreach, and Diversity Award
Awards Bioconductor Bioc2023 Recognition
5 months ago • updated 4 months ago shepherl 3.5k
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News: Bioconductor Long-term Contribution Award
Bioc2023 Bioconductor Awards Recognition
4 months ago shepherl 3.5k
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News: Nominations for Bioconductor 2023 Awards!
Awards Bioconductor Bioc2023 Recognition
5 months ago • updated 4 months ago shepherl 3.5k
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News: BioC2023 abstract submission is now open!
presentation BioC2023 Conference community Bioconductor
written 7 months ago by ▴ 30
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News: Seeking members for BioC2023 organizing committee
BioC2023 Bioconductor community
8 months ago Maria Doyle ▴ 30
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News: Save the Date Bioc2023!
Bioc2023 Conference Bioconductor
10 months ago shepherl 3.5k
11 results • Page 1 of 1
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Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
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Comment: Batch correction and repeated measures
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
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