Bioconductor Atac

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678

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rna-seq Read10X_h5 atac modalities

updated 13 months ago by James W. MacDonald 65k • written 13 months ago by Cynthia • 0

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656

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ATAC DiffBind ATACSeq

updated 14 months ago by Rory Stark ★ 5.2k • written 15 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 ★ 5.2k • written 4.0 years ago by lindsaynhayes • 0

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552

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r DiffBind ATAC

updated 4.2 years ago by Rory Stark ★ 5.2k • written 4.2 years ago by lindsaynhayes • 0

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1.4k

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limma edger atac atac-seq

updated 4.2 years ago by Aaron Lun ★ 28k • written 4.2 years ago by pgugger ▴ 70

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769

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deseq2 design formula design matrix edgeR ATAC

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

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944

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Diffbind ATAC batch correction blocking factor

updated 4.7 years ago by Rory Stark ★ 5.2k • written 4.7 years ago by rm1238 • 0

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1.8k

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ATACseqQC ATAC ATACseq software error Tutorial

updated 4.9 years ago by Steve Lianoglou ★ 13k • written 4.9 years ago by mbasam • 0

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2.9k

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subread featurecounts atac

updated 5.1 years ago by Wei Shi ★ 3.6k • written 5.1 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 ★ 5.2k • written 5.1 years ago by pgontarz ▴ 10

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2.2k

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diffbind atac

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

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4.8k

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diffbind atac

6.9 years ago niu.shengyong • 0

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4.6k

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ATAC differential binding analysis no replicates DEseq2 chromatin

7.1 years ago BioinfGuru ▴ 30

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1.4k

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Diffbind Atac adapters

updated 7.1 years ago by Rory Stark ★ 5.2k • written 7.1 years ago by BioinfGuru ▴ 30

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2.8k

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atac-seq atac deseq2 sva combat

updated 7.2 years ago by Michael Love 41k • written 7.2 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 9.0 years ago by samuel collombet ▴ 140

16 results • Page 1 of 1

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Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k

I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …

Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…

Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0

Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k

Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…

Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

Votes

Answer: DEseq2 coefficient

SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

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Scholar to Rory Stark ★ 5.2k

Popular Question to tangming2005 ▴ 190