Showing : diffbind • reset
0
votes
0
replies
37
views
Difference in Contrast in DiffBind
DiffBind
4 days ago zzrammal • 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
93
views
need help with Diffbind multiple groups
DiffBind ChIPSeqData
12 days ago Dinesh • 0
0
votes
0
replies
120
views
dba.plotProfile() plotting and interpretation
DiffBind
15 days ago Henry ▴ 10
0
votes
0
replies
92
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
16 days ago yvonneh • 0
0
votes
0
replies
87
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
16 days ago Ian D. ▴ 70
1
vote
1
reply
157
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 18 days ago by 42k • written 18 days ago by • 0
0
votes
1
reply
171
views
ATACseq merge peaks
DiffBind
updated 22 days ago by ★ 4.1k • written 24 days ago by • 0
0
votes
4
replies
267
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
2
votes
2
replies
191
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago Henry ▴ 10
0
votes
0
replies
107
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
4 weeks ago Virangika • 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
0
votes
0
replies
126
views
How to extract the coordinate of dba.plotPCA?
DiffBind PCA
7 weeks ago feather-W • 0
0
votes
0
replies
124
views
PCA plot for normalized counts using Diffbind
DiffBind PCAplot
7 weeks ago Ankit ▴ 20
0
votes
0
replies
110
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind ATACSeq
7 weeks ago Pierre Lindenbaum ▴ 10
0
votes
0
replies
150
views
Multifactor analysis in DiffBind
DiffBind multifactoranalysis
8 weeks ago erbrocato • 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
2
replies
275
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago Sam ▴ 10
0
votes
3
replies
1.2k
views
Blacklist error in DiffBind
DiffBind Blacklist
updated 10 weeks ago by • 0 • written 18 months ago by • 0
0
votes
3
replies
657
views
diffbind analyze for wheat
DiffBind
updated 11 weeks ago by • 0 • written 8 months ago by • 0
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
0
votes
4
replies
2.0k
views
Subtracting INPUT reads from ChIP read counts.
diffbind ChIP-seq
updated 3 months ago by ★ 5.2k • written 7.9 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
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
0
replies
267
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
193
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
4 months ago frueher • 0
1
vote
4
replies
1.0k
views
Diffbind error while running example data
DiffBind
written 3.2 years ago by • 0
0
votes
0
replies
183
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
4 months ago Aswathy • 0
2
votes
3
replies
655
views
Sample sheet file for DiffBind
DiffBind
updated 4 months ago by • 0 • written 11 months ago by ▴ 10
0
votes
0
replies
269
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind CUT&Tag
4 months ago Hai • 0
0
votes
0
replies
280
views
ATACseq- Counts around TSS plot
DiffBind ATACSeq
4 months ago inna.gur • 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
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
2
replies
350
views
Inconsistent results in DiffBind
DiffBind
5 months ago Sam ▴ 10
0
votes
2
replies
378
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 5 months ago by ▴ 10
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
7
replies
1.3k
views
Diffbind "No genome detected"
DiffBind
updated 5 months ago by 65k • written 11 months ago by • 0
0
votes
0
replies
348
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
6 months ago jared.andrews07 ▴ 30
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
2
replies
486
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
7 months ago r.murakami • 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
5
replies
1.2k
views
DiffBind handling of replicates and consensus
diffbind
updated 7 months ago by ★ 5.2k • written 4.3 years 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
3
votes
7
replies
884
views
Genes in open chromatin region
ChIPpeakAnno DiffBind
written 8 months ago by ▴ 10
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
1
vote
2
replies
657
views
DiffBind plot.profile y-axis unit and individual locus value on the heatmap
DiffBind
9 months ago • updated 8 months ago Junsik • 0
0
votes
2
replies
510
views
DiffBind error
DiffBind
updated 8 months ago by ★ 5.2k • written 9 months ago by • 0
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
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
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
50 results • Page 1 of 1
Recent ...
Replies
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.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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
Awards • All
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Locations • All
WEHI, Melbourne, Australia, 9 minutes ago
Russia, 13 minutes ago
Poland, 55 minutes ago
Hong Kong, 56 minutes ago
South Korea, 1 hour ago
Traffic: 386 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