Showing : Batch Correction • reset
3
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fastMNN based correction for large multi-run experiment requires a similar population set in all the individual datasets?
scrna-seq integration batch correction
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 40
0
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1
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Batch correction in Linear Models for methylation data
methylation ComBat Linear models batch correction AIC
updated 5.4 years ago by ★ 4.0k • written 5.4 years ago by • 0
5
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3
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860
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batch correction in DESeq2 > matrix not full rank > mitigate
DESeq2 batch correction
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 10
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3
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Diffbind batch effect blocking error
Diffbind ATAC batch correction blocking factor
updated 5.7 years ago by ★ 5.2k • written 5.7 years ago by • 0
1
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1
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All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 40
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Batch Correction: DESeq2 Linear Model vs Batch-Correction-Specific Algorithms (RUV, ComBat, ect.)
deseq2 differential expression batch correction
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 40
4
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Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 6.1 years ago by ▴ 150 • written 6.1 years ago by ▴ 60
7 results • Page 1 of 1
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Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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