Bioconductor Atac

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672

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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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651

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ATAC DiffBind ATACSeq

updated 14 months ago by Rory Stark ★ 5.2k • 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 ★ 5.2k • written 3.9 years ago by lindsaynhayes • 0

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548

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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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767

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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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939

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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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1.7k

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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 5.0 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 ★ 5.2k • 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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4.5k

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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 8.9 years ago by samuel collombet ▴ 140

16 results • Page 1 of 1

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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0

Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …

Answer: PCA plot suggestions by Michael Love 41k

For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10

Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…

Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k

Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…

Answer: ATACseq merge peaks by ATpoint ★ 4.0k

That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…

Votes

Answer: Math expression in shapeCustom legend in EnhancedVolcano

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length

Comment: Deseq2. decontXcounts not integers. Useful alternative?

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)

biomaRt error: database disk image is malformed

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