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 8 months ago by • 0 • written 2.8 years ago by ▴ 10
4
votes
4
replies
807
views
DESeq2 lfcShrink function used in DiffBind package
FoldChange DiffBind lfcShrink Cut&TagData
10 months ago bhandary.8590 ▴ 20
3
votes
7
replies
857
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
11 months ago Mark • 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
2
votes
2
replies
166
views
[DiffBind] Obtaining normalization factors
DiffBind
19 days ago • updated 16 days ago Henry ▴ 10
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
462
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 0
2
votes
3
replies
794
views
Getting different differentially accessible peaks between versions
dba.report DiffBind
written 11 months ago by • 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
2
votes
2
replies
378
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
20 days ago • updated 19 days ago Henry ▴ 10
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 10 weeks ago by • 0 • written 2.4 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
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
990
views
Diffbind error while running example data
DiffBind
written 3.2 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
1
reply
447
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
771
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
1
vote
2
replies
325
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 10
1
vote
2
replies
676
views
DiffBind Using edgeR: TMM Normalisation produces identical results to Library Size normalisation
DiffBind
updated 9 months ago by ★ 5.2k • written 10 months ago by • 0
1
vote
1
reply
353
views
DiffBind getting Fold values of near 0
DiffBind DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
2
replies
616
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
8 months ago Junsik • 0
1
vote
0
replies
558
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
864
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
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
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
74
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
0
replies
174
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
0
votes
1
reply
930
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
828
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
625
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
194
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
166
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
3 months ago Aswathy • 0
0
votes
0
replies
404
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
0
votes
4
replies
223
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
14 days ago • updated 12 days ago lonn • 0
0
votes
2
replies
347
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
0
votes
1
reply
561
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
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
0
replies
138
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 3.4 years ago by • 0
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
2
replies
240
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
7 weeks ago Sam ▴ 10
0
votes
0
replies
93
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
4 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
1
reply
50
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 9 hours ago by ★ 5.2k • written 23 hours ago by ▴ 70
0
votes
0
replies
108
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
4 weeks ago Ankit ▴ 20
0
votes
0
replies
108
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
4 weeks ago feather-W • 0
0
votes
0
replies
256
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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