Showing : diffBind • reset
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
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 9 months ago by • 0 • written 2.8 years ago by ▴ 10
4
votes
4
replies
817
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
3
votes
7
replies
863
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
3
votes
4
replies
1.8k
views
Errors with DiffBind, Error in peaks[, pCol]/max(peaks[, pCol]) : non-numeric argument to binary operator
DiffBind
12 months ago Mark • 0
2
votes
3
replies
615
views
Sample sheet file for DiffBind
DiffBind
updated 3 months ago by • 0 • written 10 months ago by • 0
2
votes
2
replies
171
views
[DiffBind] Obtaining normalization factors
DiffBind
22 days ago • updated 18 days ago Henry ▴ 10
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
2
votes
3
replies
1.1k
views
DiffBind does not use DESeq2 MLE estimation of fold change
DiffBind
updated 9 months ago by ★ 5.2k • written 3.1 years ago by ▴ 10
2
votes
2
replies
466
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago • updated 6 months ago r.murakami • 0
2
votes
2
replies
386
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
23 days ago • updated 22 days ago Henry ▴ 10
2
votes
3
replies
798
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 11 months ago by • 0
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 11 weeks ago by • 0 • written 2.4 years ago by • 0
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 4 months ago by ★ 5.2k • written 6.6 years ago by • 0
1
vote
7
replies
2.9k
views
Technical details of DiffBind correlation analysis
diffbind duplicatecorrelation
updated 3 months ago by ★ 5.2k • written 9.5 years ago by • 0
1
vote
4
replies
993
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by • 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
1
vote
1
reply
451
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
1
vote
2
replies
777
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
1
vote
2
replies
329
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
vote
2
replies
682
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
355
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
vote
2
replies
627
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
1
vote
0
replies
564
views
Fold values in Diffbind
DiffBind
11 months ago bhandary.8590 ▴ 20
1
vote
4
replies
1.0k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
1
vote
4
replies
873
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
1
reply
2.3k
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
1
reply
1.9k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
1
vote
1
reply
96
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
17 days ago • updated 14 days ago lonn • 0
0
votes
0
replies
499
views
Help with Diffbind result
DiffBind
11 months ago Chris • 0
0
votes
5
replies
1.2k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 12 months ago by • 0 • written 12 months ago by • 0
0
votes
1
reply
545
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
933
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
838
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
3
replies
631
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
1
reply
197
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 weeks ago • updated 6 weeks ago red_bricks ▴ 50
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
410
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
0
replies
40
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
2 days ago yvonneh • 0
0
votes
2
replies
352
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
0
votes
1
reply
566
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 11 months ago by ★ 5.2k • written 11 months ago by ▴ 10
0
votes
0
replies
33
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
2 days ago Ian D. ▴ 70
0
votes
0
replies
140
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
6 weeks ago erbrocato • 0
0
votes
5
replies
1.4k
views
DiffBind:all samples have 0 counts for all genes.
DiffBind Genrich
updated 10 months ago by • 0 • written 3.5 years ago by • 0
0
votes
1
reply
299
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind ATACSeq
3 months ago isaromero8888 • 0
0
votes
2
replies
246
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
0
votes
0
replies
98
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
5 weeks ago Pierre Lindenbaum ▴ 10
0
votes
7
replies
1.4k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
12 months ago • updated 11 months ago Ti • 0
0
votes
2
replies
116
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
3 days ago • updated 2 days ago Ian D. ▴ 70
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
France, 20 minutes ago
India, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
United States, 2 hours ago
France, 2 hours ago
Traffic: 511 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