Bioconductor ATAC

Showing : ATAC • reset

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446

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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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863

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ATAC DiffBind ATACSeq

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

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1.5k

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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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685

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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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1.8k

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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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927

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deseq2 design formula design matrix edgeR ATAC

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

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1.1k

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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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2.1k

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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 5.7 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 5.8 years ago by Rory Stark ★ 5.2k • written 5.8 years ago by paz2005 • 0

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diffbind atac

7.6 years ago • updated 7.5 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 7.8 years ago by g.atla ▴ 10

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6.6k

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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

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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