Bioconductor ATAC-Seq

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5.0k

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ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity

updated 5.2 years ago by Julie Zhu ★ 4.3k • written 5.2 years ago by Gary ▴ 20

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4.9k

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atac-seq CQN edger

updated 6.0 years ago by Aaron Lun ★ 28k • written 6.0 years ago by shankasal • 0

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1.5k

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deseq2 differential binding analysis deseq atac-seq

updated 6.2 years ago by Michael Love 41k • written 6.2 years ago by rbronste ▴ 60

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1.2k

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deseq2 atac-seq chipseq differential binding analysis

updated 6.3 years ago by Aaron Lun ★ 28k • written 6.3 years ago by rbronste ▴ 60

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5.5k

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Rsubread atac-seq narrowpeaks featurecounts

updated 6.4 years ago by Wei Shi ★ 3.6k • written 6.4 years ago by j.bergenstrahle ▴ 80

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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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1.4k

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diffbind R atac-seq

updated 5.5 years ago by Rory Stark ★ 5.1k • written 5.5 years ago by Firas • 0

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2.6k

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dba.count atac-seq diffbind

updated 6.4 years ago by Gord Brown ▴ 650 • written 6.4 years ago by ew152 • 0

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2.5k

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csaw ATAC-seq Tn5 insertions

updated 3.5 years ago by Antonio Ahn ▴ 10 • written 3.5 years ago by alexandre.blais ▴ 50

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9.2k

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atac-seq diffbind macs2 macs peak finding

updated 7.1 years ago by BioinfGuru ▴ 20 • written 7.6 years ago by igor ▴ 40

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1.2k

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CQN atac-seq normalization edgeR

5.9 years ago shankasal • 0

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1.5k

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ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ

updated 5.2 years ago by Julie Zhu ★ 4.3k • written 5.2 years ago by Gary ▴ 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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3.6k

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diffbind atac-seq

updated 7.0 years ago by Rory Stark ★ 5.1k • written 7.0 years ago by niu.shengyong • 0

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1.5k

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atac-seq diffbind

7.0 years ago zhaolin20042008 • 0

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2.7k

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diffbind chipseq atac-seq rory stark

updated 7.0 years ago by Rory Stark ★ 5.1k • written 7.0 years ago by andrew.gehrke • 0

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2.2k

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diffbind dnaseseq atac-seq

7.2 years ago rbronste ▴ 60

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2.0k

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diffbind read counting warning message chromatin atac-seq

updated 6.4 years ago by Gord Brown ▴ 650 • written 6.4 years ago by tgjohnst • 0

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2.3k

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ATAC-seq ATACseqQC

updated 4.8 years ago by Julie Zhu ★ 4.3k • written 4.8 years ago by Shuang He • 0

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1.1k

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cqn normalization conditionalquantilenormalization atac-seq

updated 4.8 years ago by Kasper Daniel Hansen ★ 6.5k • written 4.8 years ago by Eric.Martin • 0

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925

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RNA-seq DNA-seq ATAC-seq proteomics microbiome Job

4.3 years ago lhuang7 ▴ 50

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1.4k

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atacseqqc atac-seq R bioconductor rsamtools

updated 3.9 years ago by Kevin Blighe ★ 3.9k • written 3.9 years ago by rita.monteiro • 0

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1.9k

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chipseq atac-seq gro-seq bsseq rnaseq Job

8.5 years ago Jaritz,Markus ▴ 20

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3.4k

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ATACseqQC Fragmentsizedistribution ATAC-seq

3.0 years ago Xiaojie Cheng • 0

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2.6k

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atac-seq

updated 8.1 years ago by Rory Stark ★ 5.1k • written 8.1 years ago by simonjean434 ▴ 10

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1.1k

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footprinting centipede atac-seq dnaseq

7.1 years ago rbronste ▴ 60

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2.7k

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atac-seq diffbind

7.0 years ago zhaolin20042008 • 0

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2.0k

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SSH atac-seq

updated 7.0 years ago by Gord Brown ▴ 650 • written 7.0 years ago by zhaolin20042008 • 0

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1.9k

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homer atac-seq

updated 6.7 years ago by Maciej Jończyk • 0 • written 6.8 years ago by niu.shengyong • 0

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1.0k

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diffbind dba.count atac-seq

updated 6.5 years ago by Gord Brown ▴ 650 • written 6.5 years ago by VCLRAC001 • 0

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5.3k

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deseq2 atac-seq

updated 6.4 years ago by Rory Stark ★ 5.1k • written 6.4 years ago by zhongjixx • 0

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2.0k

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diffbind atac-seq dba.count

updated 6.4 years ago by Rory Stark ★ 5.1k • written 6.4 years ago by zhaolin20042008 • 0

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1.1k

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rnaseq atac-seq iso-seq chipseq Job

6.4 years ago tyler.chukwu • 0

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1.6k

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atac-seq sample size Peak Normalize

6.2 years ago jaime.alvarez.benayas • 0

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2.1k

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atac-seq software error atacseqqc

updated 6.2 years ago by Haibo.Liu • 0 • written 6.2 years ago by José Luis Lavín ▴ 10

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1.1k

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diffbind atac-seq differential analysis deseq2

updated 5.5 years ago by Rory Stark ★ 5.1k • written 5.5 years ago by duvaller • 0

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1.7k

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ATAC-Seq ChIPQC

updated 5.2 years ago by James W. MacDonald 65k • written 5.2 years ago by Subinoy Biswas ▴ 10

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2.0k

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DiffBind FRiP ATAC-Seq dba.show dba.count

updated 5.1 years ago by Rory Stark ★ 5.1k • written 5.1 years ago by Gary ▴ 20

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762

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ATACseqQC ATAC-Seq Library complexity estimateLibComplexity

5.1 years ago Gary ▴ 20

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1.9k

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ATACseqQC ATAC-seq error split bam file

updated 5.0 years ago by contact • 0 • written 5.0 years ago by Theo ▴ 10

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1.4k

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single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job

4.8 years ago • updated 4.7 years ago Julie Zhu ★ 4.3k

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941

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ATAC-seq ATACseqQC

updated 4.8 years ago by Julie Zhu ★ 4.3k • written 4.8 years ago by Shuang He • 0

42 results • Page 1 of 1

Recent ...

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Comment: Finding DEGs by using edgeR by Gordon Smyth 50k

Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …

Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0

Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…

Comment: Finding DEGs by using edgeR by prity6459 • 0

Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …

Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k

It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…

Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k

Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…

Votes

Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Comment: DEXSeq DEXSeqDataSet count matrix duplication

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

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