Bioconductor ATAC

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660

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rna-seq Read10X_h5 atac modalities

updated 12 months ago by James W. MacDonald 65k • written 12 months ago by Cynthia • 0

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640

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ATAC DiffBind ATACSeq

updated 14 months ago by Rory Stark ★ 5.1k • written 14 months ago by Hadar • 0

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1.2k

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diffbind atac

updated 3.9 years ago by Rory Stark ★ 5.1k • written 3.9 years ago by lindsaynhayes • 0

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545

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r DiffBind ATAC

updated 4.1 years ago by Rory Stark ★ 5.1k • written 4.1 years ago by lindsaynhayes • 0

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1.4k

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limma edger atac atac-seq

updated 4.1 years ago by Aaron Lun ★ 28k • written 4.1 years ago by pgugger ▴ 70

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759

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deseq2 design formula design matrix edgeR ATAC

updated 4.3 years ago by Gordon Smyth 50k • written 4.4 years ago by corinne_hutfilz • 0

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924

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Diffbind ATAC batch correction blocking factor

updated 4.7 years ago by Rory Stark ★ 5.1k • written 4.7 years ago by rm1238 • 0

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1.7k

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ATACseqQC ATAC ATACseq software error Tutorial

updated 4.8 years ago by Steve Lianoglou ★ 13k • written 4.8 years ago by mbasam • 0

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2.9k

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subread featurecounts atac

updated 5.0 years ago by Wei Shi ★ 3.6k • written 5.0 years ago by aurel.nagy ▴ 10

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1.3k

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diffbind ATACseq ATAC counts differential analysis

updated 5.1 years ago by Rory Stark ★ 5.1k • written 5.1 years ago by pgontarz ▴ 10

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diffbind atac

updated 5.2 years ago by Rory Stark ★ 5.1k • written 5.2 years ago by paz2005 • 0

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diffbind atac

6.9 years ago niu.shengyong • 0

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4.5k

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ATAC differential binding analysis no replicates DEseq2 chromatin

7.1 years ago BioinfGuru ▴ 20

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1.4k

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Diffbind Atac adapters

updated 7.1 years ago by Rory Stark ★ 5.1k • written 7.1 years ago by BioinfGuru ▴ 20

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atac-seq atac deseq2 sva combat

updated 7.1 years ago by Michael Love 41k • written 7.1 years ago by g.atla ▴ 10

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6.1k

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 8.9 years ago by Gordon Smyth 50k • written 8.9 years ago by samuel collombet ▴ 140

16 results • Page 1 of 1

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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k

As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…

Comment: Batch correction and repeated measures by Gordon Smyth 50k

In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…

Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k

I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…

Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0

Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…

Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0

Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.

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Answer: How many of my genes from my gene list are in each KEGG pathway?

Comment: Light difference when using coef vs omit a group when compare 3 groups.

DESeq2 variance transformation error and plot dispersion Estimate

A: DESeq2 variance transformation error and plot dispersion Estimate

ensembl to hgnc symbols creates duplicates

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