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ATACSeq
•
reset
0
votes
3
replies
103
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
updated 7 hours ago by
ATpoint
★ 4.0k • written 2 days ago by
lonn
• 0
0
votes
0
replies
78
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
22 days ago
Pierre Lindenbaum
▴ 10
0
votes
1
reply
279
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
12 weeks ago
isaromero8888
• 0
0
votes
0
replies
220
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
12 weeks ago
Jawahar
• 0
0
votes
0
replies
234
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
3 months ago
inna.gur
• 0
0
votes
7
replies
618
views
ATACseqQC shiftGAlignmentsList() problem
ATACseqQC
ATACSeq
updated 6 weeks ago by
danalvoronov
▴ 10 • written 4 months ago by
jfmay
• 0
0
votes
0
replies
382
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
sophie.hfliu
• 0
0
votes
2
replies
785
views
DiffBind dropping peaks in ATAC-seq data
DiffBind
ATACSeq
updated 8 months ago by
Malcolm Cook
★ 1.6k • written 8 months ago by
Nebat
• 0
4
votes
6
replies
887
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
12 months ago
Chris
• 0
3
votes
5
replies
829
views
How to annotate genes from results of DiffBind
ATACSeq
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
Chris
• 0
0
votes
2
replies
1.2k
views
long computing time for TSS enrichment score
ATACSeq
updated 7 months ago by
Noah
• 0 • written 19 months ago by
Taeim
• 0
1
vote
3
replies
1.5k
views
regionCounts() from csaw - object 'fancy_mseq' not found
ATACSeq
regionCounts
csaw
updated 4 months ago by
dineika.chandrananda
• 0 • written 23 months ago by
zgraytho88
• 0
12 results • Page
1 of 1
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Answer: Error retrieving ensembl gene id using biomaRt...
by
James W. MacDonald
65k
I can't reproduce. ``` > library(biomaRt) Warning message: package 'biomaRt' was built under R version 4.3.2 > library(org.Hs.eg.db…
Comment: DESeq2 setting significant p-value
by
Michael Love
41k
``` > counts <- matrix(1:16, ncol=4, dimnames=list(letters[1:4],NULL)) > coldata <- data.frame(x=1:4) > DESeqDataSetFromMatrix(counts, cold…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
Right, I was suggesting subsetting as a valid choice for "treatment and control samples at each timepoint"
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value
by
Dev
• 0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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