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DiFFBind
•
reset
0
votes
5
replies
215
views
Diffbind interpretation of data - fold change
DiffBind
11 days ago • updated 10 days ago
Vera
• 0
0
votes
0
replies
204
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
10 weeks ago
kim
• 0
0
votes
0
replies
155
views
diffbind covariates
DiffBind
ATACSeq
updated 11 weeks ago by
Michael Love
43k • written 11 weeks ago by
Alpesh Querer
▴ 220
0
votes
2
replies
510
views
DiffBind dba.report discrepancy
DiffBind
3 months ago • updated 12 weeks ago
aelbassiouny
• 0
0
votes
0
replies
117
views
DiffBind subset replicates
DiffBind
3 months ago
Haiping
• 0
0
votes
0
replies
196
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
3 months ago
Young Boqin
• 0
0
votes
0
replies
241
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
4 months ago
Alejandro
• 0
0
votes
2
replies
384
views
DiffBind for MBD-seq
MBD-seq
DiffBind
4 months ago
Marianna
▴ 20
0
votes
0
replies
272
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
5 months ago
Ian D.
▴ 70
0
votes
1
reply
310
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
5 months ago
mdidish
▴ 10
0
votes
0
replies
261
views
DiffBind dba.plotprofile y-axis range
DiffBind
5 months ago
Tara
• 0
0
votes
8
replies
772
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 5 months ago by
Rory Stark
★ 5.2k • written 5 months ago by
Marianna
▴ 20
1
vote
3
replies
519
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 5 months ago by
Rory Stark
★ 5.2k • written 6 months ago by
jesswhitts
• 0
0
votes
0
replies
401
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
6 months ago
gamma.jian
▴ 10
0
votes
2
replies
487
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
7 months ago
Mallory
• 0
0
votes
0
replies
274
views
Difference in Contrast in DiffBind
DiffBind
8 months ago
user_bioinfo
• 0
0
votes
0
replies
309
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
8 months ago
Dinesh
• 0
0
votes
1
reply
604
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 10 weeks ago by
B.N
• 0 • written 8 months ago by
Henry
▴ 10
0
votes
0
replies
398
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
8 months ago
yvonneh
• 0
0
votes
0
replies
303
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
8 months ago
Ian D.
▴ 70
0
votes
9
replies
1.3k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
8 months ago • updated 3 months ago
Ian D.
▴ 70
3
votes
1
reply
532
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
marcusn
▴ 10
0
votes
1
reply
814
views
ATACseq merge peaks
DiffBind
updated 8 months ago by
ATpoint
★ 4.6k • written 8 months ago by
Shloka
• 0
0
votes
4
replies
586
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
9 months ago
lonn
• 0
0
votes
0
replies
303
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
9 months ago
Virangika
• 0
2
votes
2
replies
659
views
[DiffBind] Obtaining normalization factors
DiffBind
9 months ago
Henry
▴ 10
2
votes
2
replies
1.1k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
9 months ago
Henry
▴ 10
0
votes
0
replies
398
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
9 months ago
feather-W
• 0
0
votes
0
replies
404
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
9 months ago
Ankit
▴ 20
0
votes
0
replies
365
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
9 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
395
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
10 months ago
erbrocato
• 0
0
votes
2
replies
644
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
10 months ago
Sam
▴ 10
0
votes
1
reply
489
views
Exact same results in Diffbind with different normalization methods
DiffBind
10 months ago
red_bricks
▴ 60
0
votes
1
reply
649
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
11 months ago
isaromero8888
• 0
0
votes
0
replies
664
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
12 months ago
Jawahar
• 0
0
votes
0
replies
387
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
12 months ago
frueher
• 0
0
votes
0
replies
365
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
12 months ago
Aswathy
• 0
0
votes
0
replies
533
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
12 months ago
Hai
• 0
0
votes
0
replies
473
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
12 months ago
inna.gur
• 0
0
votes
1
reply
1.3k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 12 months ago by
qq809825706
• 0 • written 17 months ago by
Mark
• 0
0
votes
2
replies
663
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 13 months ago by
Sam
▴ 10
1
vote
2
replies
575
views
Inconsistent results in DiffBind
DiffBind
13 months ago
Sam
▴ 10
1
vote
1
reply
624
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 13 months ago by
ATpoint
★ 4.6k • written 13 months ago by
Miquel
• 0
0
votes
0
replies
669
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
14 months ago
jared.andrews07
▴ 30
0
votes
0
replies
677
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 15 months ago by
James W. MacDonald
67k • written 15 months ago by
sophie.hfliu
• 0
2
votes
4
replies
1.6k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 15 months ago by
Matt Eldridge
▴ 10 • written 15 months ago by
r.murakami
• 0
2
votes
2
replies
695
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
15 months ago
r.murakami
• 0
1
vote
1
reply
804
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 15 months ago by
James W. MacDonald
67k • written 15 months ago by
lin.pei26
• 0
3
votes
7
replies
1.4k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 16 months ago by
Chris
▴ 20
0
votes
3
replies
927
views
diffbind analyze for wheat
DiffBind
updated 10 months ago by
Igor
• 0 • written 16 months ago by
zgyu12
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Problems with oarfish + tximport + swish
by
Michael Love
43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish
by
brown.annaleigh
• 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal
by
iqratechnology4
• 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
by
James W. MacDonald
67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish
by
Michael Love
43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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