Bioconductor Batch correction

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scrna-seq integration batch correction

updated 5.9 years ago by Aaron Lun ★ 29k • written 5.9 years ago by p.joshi ▴ 40

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1.7k

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methylation ComBat Linear models batch correction AIC

updated 6.0 years ago by Kevin Blighe ★ 4.0k • written 6.0 years ago by lucasmiranda42 • 0

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1.0k

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DESeq2 batch correction

updated 6.1 years ago by James W. MacDonald 68k • written 6.1 years ago by MT ▴ 10

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1.4k

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Diffbind ATAC batch correction blocking factor

updated 6.3 years ago by Rory Stark ★ 5.2k • written 6.3 years ago by rm1238 • 0

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1.4k

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deseq2 differential expression batch correction design

updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by wunderl ▴ 40

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2.1k

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deseq2 differential expression batch correction

updated 6.5 years ago by Michael Love 43k • written 6.5 years ago by wunderl ▴ 40

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2.6k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.7 years ago by Vladimir Kiselev ▴ 150 • written 6.7 years ago by hamza_karakurt ▴ 60

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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150

Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?

Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k

BTW, I tested with no issue on MacOS ARM on our previous github issue.

Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k

The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…

Answer: PTM analysis in LIMPA by Gordon Smyth 53k

For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…

Answer: problem reading bam files into nucleR by James W. MacDonald 68k

The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…

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C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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