Bioconductor ATAC

Showing : ATAC • reset

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466

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ATACSeq peaks ATAC ChIPpeakAnno

7 months ago Raghad • 0

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1.0k

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rna-seq Read10X_h5 atac modalities

updated 21 months ago by James W. MacDonald 67k • written 21 months ago by Cynthia • 0

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872

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ATAC DiffBind ATACSeq

updated 22 months ago by Rory Stark ★ 5.2k • written 23 months ago by Hadar • 0

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diffbind atac

updated 4.6 years ago by Rory Stark ★ 5.2k • written 4.6 years ago by lindsaynhayes • 0

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688

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r DiffBind ATAC

updated 4.8 years ago by Rory Stark ★ 5.2k • written 4.8 years ago by lindsaynhayes • 0

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1.9k

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limma edger atac atac-seq

updated 4.8 years ago by Aaron Lun ★ 28k • written 4.8 years ago by pgugger ▴ 70

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933

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deseq2 design formula design matrix edgeR ATAC

updated 5.0 years ago by Gordon Smyth 52k • written 5.1 years ago by corinne_hutfilz • 0

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1.2k

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Diffbind ATAC batch correction blocking factor

updated 5.4 years ago by Rory Stark ★ 5.2k • written 5.4 years ago by rm1238 • 0

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ATACseqQC ATAC ATACseq software error Tutorial

updated 5.5 years ago by Steve Lianoglou ★ 13k • written 5.5 years ago by mbasam • 0

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3.5k

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subread featurecounts atac

updated 5.7 years ago by Wei Shi ★ 3.6k • written 5.7 years ago by aurel.nagy ▴ 10

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1.6k

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diffbind ATACseq ATAC counts differential analysis

updated 5.8 years ago by Rory Stark ★ 5.2k • written 5.8 years ago by pgontarz ▴ 10

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2.5k

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diffbind atac

updated 5.9 years ago by Rory Stark ★ 5.2k • written 5.9 years ago by paz2005 • 0

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5.9k

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diffbind atac

7.6 years ago niu.shengyong ▴ 10

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5.0k

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ATAC differential binding analysis no replicates DEseq2 chromatin

7.8 years ago BioinfGuru ▴ 70

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1.5k

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Diffbind Atac adapters

updated 7.8 years ago by Rory Stark ★ 5.2k • written 7.8 years ago by BioinfGuru ▴ 70

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atac-seq atac deseq2 sva combat

updated 7.8 years ago by Michael Love 43k • written 7.9 years ago by g.atla ▴ 10

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6.7k

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 9.6 years ago by Gordon Smyth 52k • written 9.6 years ago by samuel collombet ▴ 140

17 results • Page 1 of 1

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Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0

Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…

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A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

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