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 6.4 years ago by Aaron Lun ★ 28k • written 6.4 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 7.2 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 6.5 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 ▴ 30 • written 7.7 years ago by igor ▴ 40

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1.3k

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CQN atac-seq normalization edgeR

6.0 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 4.2 years ago by Aaron Lun ★ 28k • written 4.2 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 7.1 years ago by andrew.gehrke • 0

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2.2k

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diffbind dnaseseq atac-seq

7.3 years ago • updated 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 6.5 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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933

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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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3.5k

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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 6.8 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

6.3 years ago jaime.alvarez.benayas • 0

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2.2k

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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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765

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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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951

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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 ...

Replies

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