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Showing :
diffBind
•
reset
0
votes
0
replies
111
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
17 days ago
kim
• 0
0
votes
0
replies
97
views
diffbind covariates
DiffBind
ATACSeq
updated 25 days ago by
Michael Love
42k • written 26 days ago by
Alpesh Querer
▴ 220
0
votes
2
replies
421
views
DiffBind dba.report discrepancy
DiffBind
4 weeks ago
aelbassiouny
• 0
0
votes
0
replies
86
views
DiffBind subset replicates
DiffBind
5 weeks ago
Haiping
• 0
0
votes
0
replies
135
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
6 weeks ago
Young Boqin
• 0
0
votes
0
replies
198
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
9 weeks ago
Alejandro
• 0
0
votes
2
replies
337
views
DiffBind for MBD-seq
MBD-seq
DiffBind
12 weeks ago
Marianna
▴ 20
0
votes
0
replies
226
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
3 months ago
Ian D.
▴ 70
0
votes
1
reply
264
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
3 months ago
mdidish
▴ 10
0
votes
0
replies
218
views
DiffBind dba.plotprofile y-axis range
DiffBind
3 months ago
Tara
• 0
0
votes
8
replies
694
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 3 months ago by
Rory Stark
★ 5.2k • written 3 months ago by
Marianna
▴ 20
1
vote
3
replies
443
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 4 months ago by
Rory Stark
★ 5.2k • written 4 months ago by
jesswhitts
• 0
0
votes
0
replies
339
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
4 months ago
gamma.jian
▴ 10
0
votes
2
replies
411
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
5 months ago
Mallory
• 0
0
votes
0
replies
239
views
Difference in Contrast in DiffBind
DiffBind
6 months ago
user_bioinfo
• 0
0
votes
0
replies
278
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
6 months ago
Dinesh
• 0
0
votes
1
reply
510
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 16 days ago by
B.N
• 0 • written 6 months ago by
Henry
▴ 10
0
votes
0
replies
337
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
6 months ago
yvonneh
• 0
0
votes
0
replies
271
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
6 months ago
Ian D.
▴ 70
0
votes
9
replies
1.2k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
6 months ago • updated 5 weeks ago
Ian D.
▴ 70
1
vote
1
reply
424
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 6 months ago by
Michael Love
42k • written 6 months ago by
marcusn
• 0
0
votes
1
reply
678
views
ATACseq merge peaks
DiffBind
updated 7 months ago by
ATpoint
★ 4.5k • written 7 months ago by
Shloka
• 0
0
votes
4
replies
540
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 months ago
lonn
• 0
0
votes
0
replies
262
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
7 months ago
Virangika
• 0
2
votes
2
replies
572
views
[DiffBind] Obtaining normalization factors
DiffBind
7 months ago
Henry
▴ 10
2
votes
2
replies
901
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
7 months ago
Henry
▴ 10
0
votes
0
replies
363
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
7 months ago
feather-W
• 0
0
votes
0
replies
355
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
7 months ago
Ankit
▴ 20
0
votes
0
replies
324
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
7 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
351
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 months ago
erbrocato
• 0
0
votes
2
replies
593
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
8 months ago
Sam
▴ 10
0
votes
1
reply
439
views
Exact same results in Diffbind with different normalization methods
DiffBind
8 months ago
red_bricks
▴ 60
0
votes
1
reply
575
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
10 months ago
isaromero8888
• 0
0
votes
0
replies
580
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
10 months ago
Jawahar
• 0
0
votes
0
replies
353
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
10 months ago
frueher
• 0
0
votes
0
replies
322
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
10 months ago
Aswathy
• 0
0
votes
0
replies
484
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
10 months ago
Hai
• 0
0
votes
0
replies
436
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
10 months ago
inna.gur
• 0
0
votes
1
reply
1.2k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 10 months ago by
qq809825706
• 0 • written 15 months ago by
Mark
• 0
0
votes
2
replies
606
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 11 months ago by
Sam
▴ 10
1
vote
2
replies
535
views
Inconsistent results in DiffBind
DiffBind
11 months ago
Sam
▴ 10
1
vote
1
reply
586
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 11 months ago by
ATpoint
★ 4.5k • written 11 months ago by
Miquel
• 0
0
votes
0
replies
614
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
12 months ago
jared.andrews07
▴ 30
0
votes
0
replies
621
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 13 months ago by
James W. MacDonald
67k • written 13 months ago by
sophie.hfliu
• 0
2
votes
4
replies
1.5k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 13 months ago by
Matt Eldridge
▴ 10 • written 13 months ago by
r.murakami
• 0
2
votes
2
replies
658
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
13 months ago
r.murakami
• 0
1
vote
1
reply
754
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 14 months ago by
James W. MacDonald
67k • written 14 months ago by
lin.pei26
• 0
3
votes
7
replies
1.3k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 14 months ago by
Chris
▴ 20
0
votes
3
replies
891
views
diffbind analyze for wheat
DiffBind
updated 8 months ago by
Igor
• 0 • written 14 months ago by
zgyu12
• 0
0
votes
1
reply
812
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
15 months ago
Mark
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
Paul
• 0
Unfortunately I've updated my code with the newest GRCm39 genome, and yet I am still getting the same error.... Is there anything else I ca…
Comment: WGCNA with TPM tables
by
ATpoint
★ 4.5k
WGCNA is not a Bioconductor package, but generally: If you want to do serious analysis then find the raw data. There is no guarantee what …
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
by
James W. MacDonald
67k
The `EnsDb.Mmusculus.v79` package is mm38, not mm39. If you want a current `EnsDb`, use `AnnotationHub` ``` > library(AnnotationHub) >…
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…
Comment: ANOVA like approach of edgeR
by
Yunshun Chen
▴ 880
If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …
Votes
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
A: ANOVA-like test with edgeR
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
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