Bioconductor Repeated measures

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deseq2 rnaseq repeated measures time series design formula

updated 5.0 years ago by Michael Love 43k • written 5.0 years ago by Dorien ▴ 10

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783

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deseq2 repeated measures

updated 5.1 years ago by Michael Love 43k • written 5.1 years ago by jperin • 0

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3.1k

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dream variancePartition limma differential expression repeated measures

updated 5.3 years ago by Gordon Smyth 52k • written 5.3 years ago by hermidalc ▴ 20

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1.8k

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SVA deseq2 repeated measures

updated 5.3 years ago by Robert Castelo ★ 3.4k • written 5.4 years ago by sara.blocquiaux • 0

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2.6k

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limma rna-seq mixed model repeated measures

updated 6.4 years ago by Gordon Smyth 52k • written 6.4 years ago by mikhael.manurung ▴ 280

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1.8k

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edgeR rnaseq repeated measures

updated 6.8 years ago by Ryan C. Thompson ★ 7.9k • written 6.8 years ago by wjh180 • 0

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4.5k

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deseq2 repeated measures time course

updated 7.0 years ago by Michael Love 43k • written 7.0 years ago by Marion • 0

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5.5k

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LIMMA FACTORIAL REPEATED MEASURES differential gene expression

9.4 years ago • updated 9.3 years ago robert.maughan • 0

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963

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repeated measures

9.3 years ago PJ • 0

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Comment: input for singR function by iamin053 • 0

Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!

Comment: build samplesheet and plot profile by yf • 0

![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a

Answer: I am having issues with bowtie2_build by James W. MacDonald 67k

Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…

Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k

Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…

Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Votes

A: Doubt about the "zero expression" genes or genes with no reads at all in the co

Answer: Unable to install nloptr

Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?

C: How does edgeR cpm function calculate log(CPM) values?

Answer: Selection of correct coefficients or contrasts in DESeq2

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