Bioconductor Atac

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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

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4.8k

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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 ▴ 30

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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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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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2.2k

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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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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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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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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 ▴ 30

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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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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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936

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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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762

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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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669

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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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646

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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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548

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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

16 results • Page 1 of 1

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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k

an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.

Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k

Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…

Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20

Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…

Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k

The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…

Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k

Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…

Votes

C: SGSeq: moving toward diffex from SGSeq analysis

DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds

Subset DEXSeqDataSet In DEXSeq

How to get all possible comparisons in DiffBind

Comment: get BM error

Awards • All

Scholar to ATpoint ★ 4.0k