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 ▴ 20

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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 7.1 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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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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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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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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926

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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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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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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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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

16 results • Page 1 of 1

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Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100

See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…

Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850

This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…

Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k

Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…

Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k

I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…

Answer: rlog transformation by Michael Love 41k

It is dependent on the other samples in the dataset.

Votes

Comment: DEXSeq DEXSeqDataSet count matrix duplication

Comment: Error in champ.load(): The following specified files do not exist

Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos

Using GRanges and IRanges to simply get all chromosome data

A: Using GRanges and IRanges to simply get all chromosome data

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Popular Question to W. Evan Johnson ▴ 850

Popular Question to Alejandro Reyes ★ 1.9k