Bioconductor ATAC

Showing : ATAC • reset

vote

replies

4.8k

views

diffbind atac

6.9 years ago niu.shengyong • 0

votes

replies

6.1k

views

Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 8.9 years ago by Gordon Smyth 50k • written 8.9 years ago by samuel collombet ▴ 140

votes

replies

1.4k

views

limma edger atac atac-seq

updated 4.2 years ago by Aaron Lun ★ 28k • written 4.2 years ago by pgugger ▴ 70

votes

replies

1.7k

views

ATACseqQC ATAC ATACseq software error Tutorial

updated 4.8 years ago by Steve Lianoglou ★ 13k • written 4.8 years ago by mbasam • 0

votes

replies

4.5k

views

ATAC differential binding analysis no replicates DEseq2 chromatin

7.1 years ago BioinfGuru ▴ 30

votes

replies

2.8k

views

atac-seq atac deseq2 sva combat

updated 7.2 years ago by Michael Love 41k • written 7.2 years ago by g.atla ▴ 10

votes

replies

937

views

Diffbind ATAC batch correction blocking factor

updated 4.7 years ago by Rory Stark ★ 5.1k • written 4.7 years ago by rm1238 • 0

vote

replies

1.2k

views

diffbind atac

updated 3.9 years ago by Rory Stark ★ 5.1k • written 3.9 years ago by lindsaynhayes • 0

votes

replies

2.2k

views

diffbind atac

updated 5.2 years ago by Rory Stark ★ 5.1k • written 5.2 years ago by paz2005 • 0

votes

replies

763

views

deseq2 design formula design matrix edgeR ATAC

updated 4.4 years ago by Gordon Smyth 50k • written 4.4 years ago by corinne_hutfilz • 0

votes

670

views

rna-seq Read10X_h5 atac modalities

updated 13 months ago by James W. MacDonald 65k • written 13 months ago by Cynthia • 0

vote

2.9k

views

subread featurecounts atac

updated 5.0 years ago by Wei Shi ★ 3.6k • written 5.0 years ago by aurel.nagy ▴ 10

vote

548

views

r DiffBind ATAC

updated 4.1 years ago by Rory Stark ★ 5.1k • written 4.1 years ago by lindsaynhayes • 0

votes

1.3k

views

diffbind ATACseq ATAC counts differential analysis

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

votes

646

views

ATAC DiffBind ATACSeq

updated 14 months ago by Rory Stark ★ 5.1k • written 14 months ago by Hadar • 0

votes

1.4k

views

Diffbind Atac adapters

updated 7.1 years ago by Rory Stark ★ 5.1k • written 7.1 years ago by BioinfGuru ▴ 30

16 results • Page 1 of 1

Recent ...

Replies

Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

Answer: Log-cpm values from limma

Awards • All