Bioconductor Batch correction

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1.9k

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scrna-seq integration batch correction

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by p.joshi ▴ 40

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1.3k

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methylation ComBat Linear models batch correction AIC

updated 5.1 years ago by Kevin Blighe ★ 4.0k • written 5.2 years ago by lucasmiranda42 • 0

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792

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DESeq2 batch correction

updated 5.2 years ago by James W. MacDonald 67k • written 5.2 years ago by MT ▴ 10

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1.2k

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Diffbind ATAC batch correction blocking factor

updated 5.5 years ago by Rory Stark ★ 5.2k • written 5.5 years ago by rm1238 • 0

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1.1k

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deseq2 differential expression batch correction design

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by wunderl ▴ 40

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1.7k

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deseq2 differential expression batch correction

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by wunderl ▴ 40

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2.2k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.8 years ago by Vladimir Kiselev ▴ 150 • written 5.8 years ago by hamza_karakurt ▴ 60

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Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k

Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…

Comment: Sample-specific methylation values using QSEA by User3088 • 0

Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…

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…

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Unused arguments error without used arguments in GSVA?

Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte

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?

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