Showing : diffbind • reset
0
votes
4
replies
181
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
6 days ago • updated 3 days ago lonn • 0
0
votes
0
replies
75
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
7 days ago Virangika • 0
2
votes
2
replies
143
views
[DiffBind] Obtaining normalization factors
DiffBind
11 days ago • updated 7 days ago Henry ▴ 10
2
votes
2
replies
348
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
12 days ago • updated 11 days ago Henry ▴ 10
0
votes
0
replies
96
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
25 days ago feather-W • 0
0
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0
replies
95
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
25 days ago Ankit ▴ 20
0
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0
replies
83
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DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
26 days ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
124
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
4 weeks ago erbrocato • 0
0
votes
2
replies
224
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
12 weeks ago isaromero8888 • 0
0
votes
0
replies
227
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
239
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
3 months ago inna.gur • 0
0
votes
1
reply
915
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
332
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 4 months ago by ▴ 10
1
vote
2
replies
317
views
Inconsistent results in DiffBind
DiffBind
4 months ago Sam ▴ 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
386
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
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
2
votes
2
replies
452
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
6 months ago r.murakami • 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
3
votes
7
replies
837
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 7 months ago by • 0
0
votes
3
replies
612
views
diffbind analyze for wheat
DiffBind
updated 7 weeks ago by • 0 • 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
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
2
replies
451
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
0
votes
2
replies
794
views
DiffBind dropping peaks in ATAC-seq data
DiffBind ATACSeq
updated 9 months ago by ★ 1.6k • 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
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
0
votes
5
replies
2.9k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.1k • written 9 months ago by • 0
0
votes
3
replies
605
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
5
replies
1.1k
views
DiffBind handling of replicates and consensus
diffbind
updated 6 months ago by ★ 5.1k • written 4.2 years ago by • 0
1
vote
4
replies
826
views
diffbind dba.count error "files could not be accessed" on windows 11
DiffBind
9 months ago Theo ▴ 10
1
vote
2
replies
663
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
0
votes
1
reply
534
views
DiffBind output issues
DiffBind
updated 10 months ago by ★ 5.1k • written 10 months ago by • 0
1
vote
2
replies
749
views
Interpret plots from DiffBind
DiffBind
10 months ago Chris • 0
2
votes
3
replies
598
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
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
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
0
votes
0
replies
400
views
Title in dba.plotProfile
DiffBind
10 months ago agata17 • 0
0
votes
1
reply
551
views
dba.count with pre-defined regions produced only 10% results
DiffBind diffbind
updated 11 months ago by ★ 5.1k • written 11 months ago by ▴ 10
0
votes
1
reply
646
views
DiffBind dba() in parallel
DiffBind
updated 11 months ago by ★ 5.1k • written 11 months ago by • 0
1
vote
4
replies
995
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
50 results • Page 1 of 1
Recent ...
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Answer: List of Deprecated Packages for Bioc3.19 by shepherl 3.8k
singleCellTK has been fixed and will remain in Bioconductor
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Yes, I'm working only with genes from terpenoids pathway (14 genes), so I can't use enrichGO? Can you recommend a package or something like…
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
Your awnser at Cannabis orgDb solve my problems using enrichGO by far. I'm underdegree biotechnology student, and I learning bioinformatic…
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
It is indeed better. Anyway, did you notice this part in the output from `str(ortologos_filtrados)`: `$Gene.ID : int 115709372 115716460 …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
I'm new here, but its better now?
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Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
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