Showing : diffbind • reset
8
votes
13
replies
1.9k
views
Interpret plot from DiffBind
DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by ▴ 10
5
votes
19
replies
6.0k
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
847
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
11 months ago • updated 10 months ago bhandary.8590 ▴ 20
3
votes
7
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884
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 3 months ago by • 0 • written 2.4 years ago by • 0
2
votes
2
replies
191
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago Henry ▴ 10
2
votes
2
replies
486
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 0
2
votes
4
replies
1.3k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 7 months ago by • 0 • written 7 months ago by • 0
2
votes
3
replies
808
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 12 months ago by • 0
2
votes
2
replies
417
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
5 weeks ago Henry ▴ 10
2
votes
3
replies
655
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
2
votes
3
replies
1.2k
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
1
vote
3
replies
1.9k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 5 months ago by ★ 5.2k • written 6.6 years ago by • 0
1
vote
7
replies
3.0k
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
1.0k
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by • 0
1
vote
7
replies
1.3k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
1
vote
1
reply
472
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
828
views
Interpret plots from DiffBind
DiffBind
11 months ago • updated 10 months ago Chris ▴ 10
1
vote
2
replies
351
views
Inconsistent results in DiffBind
DiffBind
5 months ago Sam ▴ 10
1
vote
2
replies
712
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
377
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
658
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago Junsik • 0
1
vote
0
replies
588
views
Fold values in Diffbind
DiffBind
12 months ago bhandary.8590 ▴ 20
1
vote
4
replies
1.1k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 11 months ago by ★ 5.2k • written 12 months ago by • 0
1
vote
4
replies
908
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
10 months ago Theo ▴ 10
1
vote
1
reply
2.4k
views
Question regarding lfcShrink types in DiffBind
FoldChange DiffBind lfcShrink
updated 9 months ago by ★ 5.2k • written 10 months ago by ▴ 20
1
vote
1
reply
2.0k
views
Help with error DiffBind
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by ▴ 10
1
vote
1
reply
157
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
0
votes
4
replies
269
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 29 days ago lonn • 0
0
votes
1
reply
569
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
958
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
879
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
675
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
215
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago red_bricks ▴ 50
0
votes
0
replies
184
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
4 months ago Aswathy • 0
0
votes
0
replies
429
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
92
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
17 days ago yvonneh • 0
0
votes
2
replies
379
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
0
votes
1
reply
575
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 11 months ago by ★ 5.2k • written 12 months ago by ▴ 10
0
votes
0
replies
87
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
17 days ago Ian D. ▴ 70
0
votes
0
replies
150
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
8 weeks ago erbrocato • 0
0
votes
5
replies
1.4k
views
DiffBind:all samples have 0 counts for all genes.
DiffBind Genrich
updated 11 months ago by • 0 • written 3.5 years ago by • 0
0
votes
1
reply
327
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
275
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago Sam ▴ 10
0
votes
0
replies
39
views
Difference in Contrast in DiffBind
DiffBind
4 days ago zzrammal • 0
0
votes
0
replies
112
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
7 weeks ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
94
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
12 days ago Dinesh • 0
0
votes
7
replies
1.4k
views
DiffBind - question about showing significant difference on peaks with 0 fold change
DiffBind
13 months ago • updated 11 months ago Ti • 0
0
votes
4
replies
375
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 7 days ago by • 0 • written 18 days ago by ▴ 70
0
votes
0
replies
124
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
7 weeks ago Ankit ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
Thank you for advice, you mean I need to add: countdata_rat <- data.frame(condition = as.factor(METADATA_RAT$treatment)) and total: dds_…
Answer: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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