Bioconductor ATAC

Showing : ATAC • reset

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923

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ATACSeq peaks ATAC ChIPpeakAnno

17 months ago Raghad • 0

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1.5k

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rna-seq Read10X_h5 atac modalities

updated 2.6 years ago by James W. MacDonald 68k • written 2.6 years ago by Cynthia • 0

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1.2k

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ATAC DiffBind ATACSeq

updated 2.7 years ago by Rory Stark ★ 5.2k • written 2.7 years ago by Hadar • 0

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1.8k

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diffbind atac

updated 5.5 years ago by Rory Stark ★ 5.2k • written 5.5 years ago by lindsaynhayes • 0

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840

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r DiffBind ATAC

updated 5.7 years ago by Rory Stark ★ 5.2k • written 5.7 years ago by lindsaynhayes • 0

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2.3k

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limma edger atac atac-seq

updated 5.7 years ago by Aaron Lun ★ 29k • written 5.7 years ago by pgugger ▴ 70

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1.2k

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deseq2 design formula design matrix edgeR ATAC

updated 5.9 years ago by Gordon Smyth 53k • written 5.9 years ago by corinne_hutfilz • 0

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Diffbind ATAC batch correction blocking factor

updated 6.2 years ago by Rory Stark ★ 5.2k • written 6.2 years ago by rm1238 • 0

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2.5k

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ATACseqQC ATAC ATACseq software error Tutorial

updated 6.4 years ago by Steve Lianoglou ★ 13k • written 6.4 years ago by mbasam • 0

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4.1k

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subread featurecounts atac

updated 6.6 years ago by Wei Shi ★ 3.6k • written 6.6 years ago by aurel.nagy ▴ 10

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1.9k

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diffbind ATACseq ATAC counts differential analysis

updated 6.6 years ago by Rory Stark ★ 5.2k • written 6.6 years ago by pgontarz ▴ 10

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2.8k

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diffbind atac

updated 6.7 years ago by Rory Stark ★ 5.2k • written 6.7 years ago by paz2005 • 0

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6.9k

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diffbind atac

8.4 years ago niu.shengyong ▴ 10

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5.6k

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ATAC differential binding analysis no replicates DEseq2 chromatin

8.6 years ago BioinfGuru ▴ 70

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1.7k

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Diffbind Atac adapters

updated 8.6 years ago by Rory Stark ★ 5.2k • written 8.6 years ago by BioinfGuru ▴ 70

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atac-seq atac deseq2 sva combat

updated 8.7 years ago by Michael Love 43k • written 8.7 years ago by g.atla ▴ 10

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7.2k

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 10.4 years ago by Gordon Smyth 53k • written 10.5 years ago by samuel collombet ▴ 140

17 results • Page 1 of 1

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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112

Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

we can investigate this issue. thank you for bringing it to our attention

Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

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Bioconductor 3.22 Released!

Comment: "Watched Tags" are being erased rather than updated

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

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