Showing : zinbwave • reset
4
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3
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458
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Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 12 months ago by ★ 27k • written 12 months ago by ▴ 20
3
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3
replies
447
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Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 22 months ago by 37k • written 22 months ago by ▴ 20
1
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4
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532
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How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA zinbwave batch IntegratedData
updated 20 months ago by ▴ 890 • written 20 months ago by ★ 1.5k
0
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2
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1.5k
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cmdscale() error: NA values not allowed in 'd', ask for help.
cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq
updated 22 months ago by ▴ 890 • written 23 months ago by ▴ 10
0
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1
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484
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merging RUV-corrected datasets in DESEq
deseq2 glm zinbwave ruvseq
updated 3.4 years ago by 37k • written 3.4 years ago by ▴ 50
0
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0
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238
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contradicting behavior after in low-dimensional representation with zinbwave
zinbwave PCA
19 months ago Assa Yeroslaviz ★ 1.5k
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5
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ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2 ZINB zinbwave deseq
updated 15 months ago by 37k • written 15 months ago by • 0
0
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2
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1.1k
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How to overcome negative values obtained from vst for downstream analysis ( calculating bray-curtis and PCoA plot)?
zinbwave deseq2 vegan
updated 2.5 years ago by 59k • written 2.5 years ago by • 0
8 results • Page 1 of 1
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Comment: CPM after RUVseq by James W. MacDonald 59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq by James W. MacDonald 59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq by Jess • 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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