Showing : DiffBind • reset
0
votes
0
replies
11
views
ATACseq merge peaks
DiffBind
1 hour ago • updated 31 minutes ago Shloka • 0
0
votes
4
replies
191
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
7 days ago • updated 4 days ago lonn • 0
0
votes
0
replies
76
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
8 days ago Virangika • 0
2
votes
2
replies
143
views
[DiffBind] Obtaining normalization factors
DiffBind
12 days ago • updated 8 days ago Henry ▴ 10
2
votes
2
replies
351
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
12 days ago Henry ▴ 10
0
votes
0
replies
96
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
26 days ago feather-W • 0
0
votes
0
replies
95
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
26 days ago Ankit ▴ 20
0
votes
0
replies
83
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
27 days ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
125
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
5 weeks ago erbrocato • 0
0
votes
2
replies
227
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 weeks ago • updated 5 weeks ago Sam ▴ 10
0
votes
1
reply
185
views
Exact same results in Diffbind with different normalization methods
DiffBind
6 weeks ago • updated 5 weeks ago red_bricks ▴ 50
0
votes
1
reply
285
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
votes
0
replies
229
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
0
votes
0
replies
164
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
0
votes
0
replies
155
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
0
votes
0
replies
221
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
3 months ago Hai • 0
0
votes
0
replies
240
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
1
vote
2
replies
317
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
0
votes
2
replies
333
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
vote
1
reply
338
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
0
votes
0
replies
319
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
0
votes
0
replies
387
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 6 months ago by 65k • written 6 months ago by • 0
2
votes
2
replies
453
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 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 6 months ago by • 0 • written 6 months ago by • 0
1
vote
1
reply
432
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 65k • written 6 months ago by • 0
0
votes
3
replies
613
views
diffbind analyze for wheat
DiffBind
updated 7 weeks ago by • 0 • written 7 months ago by • 0
3
votes
7
replies
838
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
votes
1
reply
531
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago Mark • 0
0
votes
1
reply
916
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 3 months ago by • 0 • written 8 months ago by • 0
0
votes
2
replies
454
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
1
vote
2
replies
595
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
0
votes
3
replies
606
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
0
votes
2
replies
795
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • written 9 months ago by • 0
0
votes
5
replies
2.9k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
1
vote
1
reply
2.2k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.1k • written 9 months ago by ▴ 20
1
vote
4
replies
831
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
664
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
2
votes
3
replies
599
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
votes
4
replies
790
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
1
vote
2
replies
749
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
0
votes
1
reply
534
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.1k • written 10 months ago by • 0
0
votes
0
replies
417
views
Help with error running DiffBind
DiffBind
10 months ago Chris • 0
1
vote
7
replies
1.2k
views
Diffbind "No genome detected"
DiffBind
updated 4 months ago by 65k • written 10 months ago by • 0
0
votes
0
replies
400
views
Title in dba.plotProfile
DiffBind
10 months ago agata17 • 0
7
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
1
vote
4
replies
996
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
1
vote
0
replies
549
views
Fold values in Diffbind
DiffBind
11 months ago bhandary.8590 ▴ 20
0
votes
1
reply
646
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.1k • written 11 months ago by • 0
2
votes
3
replies
773
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 11 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by marka • 0
As a single dad in Australia, finding time to unwind is rare, but [Lincoln Casino][1] has become my go-to escape after putting the kids to …
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.
Comment: 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…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
Awards • All
Popular Question to Bine ▴ 40
Scholar to ATpoint ★ 4.0k
Popular Question to Gordon Smyth 50k
Popular Question to i.sudbery ▴ 40
Scholar to Michael Love 41k
Locations • All
United States, 4 minutes ago
United States, 6 minutes ago
India, 8 minutes ago
United States, 9 minutes ago
San Diego, 10 minutes ago
Traffic: 824 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6