Bioconductor Atac-seq

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ATAC-seq DESeq2 Oddresults

updated 9 weeks ago by ATpoint ★ 4.6k • written 11 weeks ago by Ricardo Iván • 0

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4.4k

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ATACseqQC Fragmentsizedistribution ATAC-seq

3.7 years ago • updated 3.6 years ago Xiaojie Cheng • 0

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3.1k

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csaw ATAC-seq Tn5 insertions

updated 4.1 years ago by Antonio Ahn ▴ 10 • written 4.2 years ago by alexandre.blais ▴ 50

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1.7k

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atacseqqc atac-seq R bioconductor rsamtools

updated 4.6 years ago by Kevin Blighe ★ 4.0k • written 4.6 years ago by rita.monteiro • 0

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1.8k

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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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1.1k

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

5.0 years ago lhuang7 ▴ 50

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1.6k

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

5.5 years ago • updated 5.3 years ago Julie Zhu ★ 4.3k

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1.3k

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cqn normalization conditionalquantilenormalization atac-seq

updated 5.4 years ago by Kasper Daniel Hansen ★ 6.5k • written 5.4 years ago by Eric.Martin • 0

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2.8k

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ATAC-seq ATACseqQC

updated 5.4 years ago by Julie Zhu ★ 4.3k • written 5.4 years ago by Shuang He • 0

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1.2k

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ATAC-seq ATACseqQC

updated 5.4 years ago by Julie Zhu ★ 4.3k • written 5.4 years ago by Shuang He • 0

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2.2k

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ATACseqQC ATAC-seq error split bam file

updated 5.6 years ago by contact • 0 • written 5.6 years ago by Theo ▴ 10

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2.4k

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DiffBind FRiP ATAC-Seq dba.show dba.count

updated 5.7 years ago by Rory Stark ★ 5.2k • written 5.8 years ago by Gary ▴ 20

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928

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ATACseqQC ATAC-Seq Library complexity estimateLibComplexity

5.8 years ago Gary ▴ 20

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1.7k

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ATACseqQC bamQC ATAC-Seq totalQNAMEs MAPQ

updated 5.8 years ago by Julie Zhu ★ 4.3k • written 5.8 years ago by Gary ▴ 20

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5.9k

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ATACseqQC ATAC-Seq quality analysis fragment size distribution library complexity

updated 5.9 years ago by Julie Zhu ★ 4.3k • written 5.9 years ago by Gary ▴ 20

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2.1k

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ATAC-Seq ChIPQC

updated 5.9 years ago by James W. MacDonald 67k • written 5.9 years ago by Subinoy Biswas ▴ 10

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1.4k

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diffbind atac-seq differential analysis deseq2

updated 6.1 years ago by Rory Stark ★ 5.2k • written 6.1 years ago by duvaller • 0

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1.6k

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diffbind R atac-seq

updated 6.2 years ago by Rory Stark ★ 5.2k • written 6.2 years ago by Firas • 0

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1.5k

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CQN atac-seq normalization edgeR

6.6 years ago shankasal • 0

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5.9k

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atac-seq CQN edger

updated 6.6 years ago by Aaron Lun ★ 28k • written 6.6 years ago by shankasal • 0

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2.5k

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atac-seq software error atacseqqc

updated 6.8 years ago by Haibo.Liu • 0 • written 6.9 years ago by José Luis Lavín ▴ 10

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1.8k

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deseq2 differential binding analysis deseq atac-seq

updated 6.9 years ago by Michael Love 43k • written 6.9 years ago by rbronste ▴ 60

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1.9k

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atac-seq sample size Peak Normalize

6.9 years ago jaime.alvarez.benayas • 0

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1.4k

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deseq2 atac-seq chipseq differential binding analysis

updated 7.0 years ago by Aaron Lun ★ 28k • written 7.0 years ago by rbronste ▴ 60

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1.3k

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rnaseq atac-seq iso-seq chipseq Job

7.0 years ago tyler.chukwu • 0

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2.3k

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diffbind atac-seq dba.count

updated 7.1 years ago by Rory Stark ★ 5.2k • written 7.1 years ago by zhaolin20042008 • 0

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6.2k

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deseq2 atac-seq

updated 7.1 years ago by Rory Stark ★ 5.2k • written 7.1 years ago by zhongjixx • 0

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6.2k

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Rsubread atac-seq narrowpeaks featurecounts

updated 7.1 years ago by Wei Shi ★ 3.6k • written 7.1 years ago by j.bergenstrahle ▴ 90

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2.3k

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diffbind read counting warning message chromatin atac-seq

updated 7.1 years ago by Gord Brown ▴ 670 • written 7.1 years ago by tgjohnst • 0

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3.1k

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dba.count atac-seq diffbind

updated 7.1 years ago by Gord Brown ▴ 670 • written 7.1 years ago by ew152 • 0

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1.2k

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diffbind dba.count atac-seq

updated 7.2 years ago by Gord Brown ▴ 670 • written 7.2 years ago by VCLRAC001 • 0

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2.3k

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homer atac-seq

updated 7.4 years ago by Maciej Jończyk • 0 • written 7.5 years ago by niu.shengyong ▴ 10

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2.3k

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SSH atac-seq

updated 7.6 years ago by Gord Brown ▴ 670 • written 7.6 years ago by zhaolin20042008 • 0

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4.1k

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diffbind atac-seq

updated 7.7 years ago by Rory Stark ★ 5.2k • written 7.7 years ago by niu.shengyong ▴ 10

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3.1k

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atac-seq diffbind

7.7 years ago zhaolin20042008 • 0

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1.7k

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atac-seq diffbind

7.7 years ago zhaolin20042008 • 0

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3.0k

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diffbind chipseq atac-seq rory stark

updated 7.7 years ago by Rory Stark ★ 5.2k • written 7.7 years ago by andrew.gehrke • 0

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1.3k

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footprinting centipede atac-seq dnaseq

7.7 years ago rbronste ▴ 60

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9.8k

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atac-seq diffbind macs2 macs peak finding

updated 7.8 years ago by BioinfGuru ▴ 70 • written 8.3 years ago by igor ▴ 50

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3.2k

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atac-seq atac deseq2 sva combat

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

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2.5k

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diffbind dnaseseq atac-seq

7.9 years ago rbronste ▴ 60

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2.9k

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atac-seq

updated 8.8 years ago by Rory Stark ★ 5.2k • written 8.8 years ago by simonjean434 ▴ 10

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2.1k

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chipseq atac-seq gro-seq bsseq rnaseq Job

9.1 years ago Jaritz,Markus ▴ 20

43 results • Page 1 of 1

Recent ...

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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Thanks for your reply!

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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