Showing : diffBind • reset
0
votes
0
replies
17
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
10 hours ago yvonneh • 0
0
votes
0
replies
15
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
10 hours ago Ian D. ▴ 70
0
votes
2
replies
88
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 10 hours ago Ian D. ▴ 70
1
vote
1
reply
81
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
1
reply
114
views
ATACseq merge peaks
DiffBind
updated 6 days ago by ★ 4.1k • written 8 days ago by • 0
0
votes
4
replies
229
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 days ago • updated 12 days ago lonn • 0
0
votes
0
replies
93
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
17 days ago Virangika • 0
2
votes
2
replies
166
views
[DiffBind] Obtaining normalization factors
DiffBind
20 days ago • updated 16 days ago Henry ▴ 10
2
votes
2
replies
379
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
21 days ago • updated 20 days ago Henry ▴ 10
0
votes
0
replies
109
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
4 weeks ago feather-W • 0
0
votes
0
replies
109
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
4 weeks ago Ankit ▴ 20
0
votes
0
replies
93
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
5 weeks ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
138
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
6 weeks ago erbrocato • 0
0
votes
2
replies
242
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
0
votes
1
reply
194
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago red_bricks ▴ 50
0
votes
1
reply
297
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
244
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
175
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
0
votes
0
replies
168
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
0
votes
0
replies
237
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
4 months ago Hai • 0
0
votes
0
replies
256
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
1
vote
2
replies
326
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
0
votes
2
replies
349
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
vote
1
reply
354
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
0
replies
330
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
405
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
463
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago • updated 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 7 months ago by • 0
1
vote
1
reply
448
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
3
replies
631
views
diffbind analyze for wheat
DiffBind
updated 9 weeks ago by • 0 • written 7 months ago by • 0
3
votes
7
replies
857
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
votes
1
reply
543
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
931
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by • 0 • written 8 months ago by • 0
0
votes
2
replies
481
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 8 months ago by • 0
1
vote
2
replies
617
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
0
votes
3
replies
627
views
DiffBind issue with edgeR$bTagwise and DESeq2$fitType
Config DiffBind Error
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
0
votes
2
replies
833
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
3.0k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • 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 ★ 5.2k • written 9 months ago by ▴ 20
1
vote
4
replies
866
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
678
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
1
vote
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
2
votes
3
replies
608
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
4
votes
4
replies
809
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
1
vote
2
replies
772
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
0
votes
1
reply
544
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
0
votes
0
replies
428
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 5 months ago by 65k • written 11 months ago by • 0
0
votes
0
replies
410
views
Title in dba.plotProfile
DiffBind
11 months ago agata17 • 0
8
votes
13
replies
1.9k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by ★ 5.2k • written 11 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards • All
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Popular Question to shepherl 3.9k
Popular Question to siajunren • 0
Scholar to Rory Stark ★ 5.2k
Locations • All
France, 4 minutes ago
WEHI, Melbourne, Australia, 21 minutes ago
St Louis, MO, 1 hour ago
United States, 2 hours ago
United States, 3 hours ago
Traffic: 599 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