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Showing :
DiFFBind
•
reset
0
votes
0
replies
111
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
16 days ago
kim
• 0
0
votes
0
replies
96
views
diffbind covariates
DiffBind
ATACSeq
updated 24 days ago by
Michael Love
42k • written 25 days ago by
Alpesh Querer
▴ 220
0
votes
2
replies
421
views
DiffBind dba.report discrepancy
DiffBind
4 weeks ago • updated 29 days 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
197
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
693
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
442
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
509
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 15 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 4 weeks ago
Ian D.
▴ 70
1
vote
1
reply
423
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 6 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
571
views
[DiffBind] Obtaining normalization factors
DiffBind
7 months ago
Henry
▴ 10
2
votes
2
replies
898
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
438
views
Exact same results in Diffbind with different normalization methods
DiffBind
8 months ago
red_bricks
▴ 60
0
votes
1
reply
574
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
657
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
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Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di
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James W. MacDonald
67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA
by
Kent
• 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
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67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
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67k
It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install `HilbertVis` on my work box…
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