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Diffbind
•
reset
8
votes
13
replies
2.6k
views
Help with Error in DiffBind
DiffBind
ATACSeq
12 months ago
Chris
• 0
7
votes
13
replies
1.7k
views
Interpret plot from DiffBind
DiffBind
updated 9 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
Chris
• 0
5
votes
19
replies
5.7k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 7 months ago by
liz.lamarca
• 0 • written 2.7 years ago by
kwangbom
▴ 10
4
votes
4
replies
743
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange
DiffBind
lfcShrink
Cut&TagData
9 months ago
bhandary.8590
▴ 20
4
votes
6
replies
861
views
Positive and negative value fold value in ATAC seq using DiffBind
DiffBind
ATACSeq
11 months ago
Chris
• 0
3
votes
7
replies
792
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 6 months ago by
Chris
• 0
3
votes
4
replies
1.7k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
10 months ago
Mark
• 0
2
votes
3
replies
1.1k
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 3.0 years ago by
Sam
▴ 10
2
votes
3
replies
728
views
Getting different differentially accessible peaks between versions
dba.report
DiffBind
written 10 months ago by
jandrade
• 0
2
votes
1
reply
545
views
how diffbind count the reads of each peak in each sample?
diffbind
DiffBind
updated 11 months ago by
Rory Stark
★ 5.1k • written 11 months ago by
hfyuan2016
• 0
2
votes
3
replies
560
views
Sample sheet file for DiffBind
DiffBind
updated 11 weeks ago by
meghanapple2
• 0 • written 9 months ago by
Chris
• 0
2
votes
4
replies
1.2k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 5 weeks ago by
marcusn
• 0 • written 2.3 years ago by
bhanu.chandra1
• 0
2
votes
4
replies
1.2k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 5 months ago by
Matt Eldridge
• 0 • written 5 months ago by
r.murakami
• 0
2
votes
2
replies
423
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
5 months ago
r.murakami
• 0
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind
R
chipseq
updated 3 months ago by
Rory Stark
★ 5.1k • written 6.5 years ago by
kyliecode
• 0
1
vote
7
replies
2.8k
views
Technical details of DiffBind correlation analysis
diffbind
duplicatecorrelation
updated 9 weeks ago by
Rory Stark
★ 5.1k • written 9.4 years ago by
meisan406
• 0
1
vote
4
replies
941
views
Diffbind error while running example data
DiffBind
written 3.1 years ago by
Lucky
• 0
1
vote
7
replies
1.1k
views
Diffbind "No genome detected"
DiffBind
updated 4 months ago by
James W. MacDonald
65k • written 9 months ago by
kyliecode
• 0
1
vote
1
reply
391
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
lin.pei26
• 0
1
vote
2
replies
704
views
Interpret plots from DiffBind
DiffBind
9 months ago
Chris
• 0
1
vote
2
replies
274
views
Inconsistent results in DiffBind
DiffBind
3 months ago
Sam
▴ 10
1
vote
2
replies
622
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
Stevie Pederson
• 0
1
vote
1
reply
291
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
Miquel
• 0
1
vote
2
replies
556
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
7 months ago
Junsik
• 0
1
vote
0
replies
517
views
Fold values in Diffbind
DiffBind
10 months ago
bhandary.8590
▴ 20
1
vote
4
replies
921
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
lin.pei26
• 0
1
vote
1
reply
2.0k
views
Question regarding lfcShrink types in DiffBind
FoldChange
DiffBind
lfcShrink
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
bhandary.8590
▴ 20
1
vote
1
reply
1.7k
views
Help with error DiffBind
DiffBind
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
Chris
• 0
0
votes
0
replies
444
views
Help with Diffbind result
DiffBind
10 months ago
Chris
• 0
0
votes
5
replies
1.1k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 10 months ago by
householdelsewhere
• 0 • written 11 months ago by
Oscar
• 0
0
votes
0
replies
125
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
10 weeks ago
frueher
• 0
0
votes
1
reply
878
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by
qq809825706
• 0 • written 7 months ago by
Mark
• 0
0
votes
2
replies
741
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
0
votes
3
replies
549
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config
DiffBind
Error
updated 8 months ago by
Rory Stark
★ 5.1k • written 8 months ago by
jason.kost
• 0
0
votes
1
reply
143
views
Exact same results in Diffbind with different normalization methods
DiffBind
16 days ago • updated 11 days ago
red_bricks
▴ 50
0
votes
0
replies
359
views
Title in dba.plotProfile
DiffBind
10 months ago
agata17
• 0
0
votes
0
replies
342
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
sophie.hfliu
• 0
0
votes
0
replies
130
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
10 weeks ago
Aswathy
• 0
0
votes
1
reply
527
views
dba.count with pre-defined regions produced only 10% results
DiffBind
diffbind
updated 10 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
littlefishes20
▴ 10
0
votes
1
reply
494
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
7 months ago
Mark
• 0
0
votes
4
replies
752
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
8 months ago
Theo
• 0
0
votes
5
replies
1.3k
views
DiffBind:all samples have 0 counts for all genes.
DiffBind
Genrich
updated 9 months ago by
xm00262
• 0 • written 3.4 years ago by
peris_baba
• 0
0
votes
1
reply
241
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
9 weeks ago
isaromero8888
• 0
0
votes
2
replies
175
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
16 days ago • updated 14 days ago
Sam
▴ 10
0
votes
0
replies
21
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
13 hours ago
Pierre Lindenbaum
▴ 10
0
votes
7
replies
1.3k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
11 months ago • updated 10 months ago
Ti
• 0
0
votes
5
replies
1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 6 months ago by
Rory Stark
★ 5.1k • written 4.1 years ago by
Jim
• 0
0
votes
2
replies
297
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 3 months ago by
Sam
▴ 10
0
votes
0
replies
203
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
3 months ago
inna.gur
• 0
0
votes
1
reply
477
views
Plotting read densities from DiffBind results
Read
density
DiffBind
updated 11 months ago by
Rory Stark
★ 5.1k • written 11 months ago by
bhandary.8590
▴ 20
50 results • Page
1 of 1
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May be documented by the software you are using? https://github.com/lpantano/DEGreport
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Yes that is correct
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