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DiFFBind
•
reset
1
vote
9
replies
3.0k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.0 years ago by
Oscar
▴ 10
0
votes
0
replies
125
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
13 days ago
atlanta
• 0
0
votes
4
replies
2.0k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
17 days ago • updated 6 days ago
Mengjun
• 0
0
votes
0
replies
65
views
DiffBind multi-tissue comparison
DiffBind
5 weeks ago
lryrainche
• 0
1
vote
8
replies
2.3k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
6 weeks ago • updated 15 days ago
Luca
• 0
0
votes
0
replies
128
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
7 weeks ago
Harish
• 0
0
votes
4
replies
1.1k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 7 weeks ago by
Harry
• 0 • written 7 weeks ago by
tifaGis
• 0
0
votes
1
reply
169
views
building samplesheet and plot profile
DiffBind
12 weeks ago • updated 11 weeks ago
yf
• 0
0
votes
5
replies
457
views
Diffbind interpretation of data - fold change
DiffBind
3 months ago
Vera
• 0
0
votes
0
replies
355
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
5 months ago
kim
• 0
0
votes
0
replies
251
views
diffbind covariates
DiffBind
ATACSeq
updated 5 months ago by
Michael Love
43k • written 6 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
718
views
DiffBind dba.report discrepancy
DiffBind
6 months ago
aelbassiouny
• 0
0
votes
0
replies
180
views
DiffBind subset replicates
DiffBind
6 months ago
Haiping
• 0
0
votes
0
replies
357
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
6 months ago
Young Boqin
• 0
0
votes
0
replies
318
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
7 months ago
Alejandro
• 0
0
votes
2
replies
472
views
DiffBind for MBD-seq
MBD-seq
DiffBind
7 months ago
Marianna
▴ 20
0
votes
1
reply
544
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
8 months ago • updated 10 weeks ago
Ian D.
▴ 70
0
votes
1
reply
411
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
8 months ago
mdidish
▴ 10
0
votes
0
replies
337
views
DiffBind dba.plotprofile y-axis range
DiffBind
8 months ago
Tara
• 0
0
votes
8
replies
975
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 8 months ago by
Rory Stark
★ 5.2k • written 8 months ago by
Marianna
▴ 20
1
vote
3
replies
682
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
jesswhitts
• 0
0
votes
0
replies
513
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
10 months ago
gamma.jian
▴ 10
0
votes
2
replies
674
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
10 months ago
Mallory
• 0
0
votes
0
replies
357
views
Difference in Contrast in DiffBind
DiffBind
11 months ago
user_bioinfo
• 0
0
votes
0
replies
376
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 months ago
Dinesh
• 0
0
votes
1
reply
767
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 5 months ago by
B.N
• 0 • written 11 months ago by
Henry
▴ 10
0
votes
0
replies
518
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
11 months ago
yvonneh
• 0
0
votes
0
replies
355
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
11 months ago
Ian D.
▴ 70
0
votes
9
replies
1.5k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
11 months ago • updated 6 months ago
Ian D.
▴ 70
3
votes
1
reply
702
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 11 months ago by
Michael Love
43k • written 11 months ago by
marcusn
▴ 10
0
votes
1
reply
1.1k
views
ATACseq merge peaks
DiffBind
updated 12 months ago by
ATpoint
★ 4.8k • written 12 months ago by
Shloka
• 0
0
votes
4
replies
697
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
12 months ago
lonn
• 0
0
votes
0
replies
376
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
12 months ago
Virangika
• 0
2
votes
2
replies
821
views
[DiffBind] Obtaining normalization factors
DiffBind
12 months ago
Henry
▴ 10
2
votes
2
replies
1.3k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
12 months ago
Henry
▴ 10
0
votes
0
replies
478
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
13 months ago
feather-W
• 0
0
votes
0
replies
499
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
13 months ago
Ankit
▴ 20
0
votes
0
replies
451
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
13 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
461
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
13 months ago
erbrocato
• 0
0
votes
2
replies
747
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
13 months ago
Sam
▴ 10
0
votes
1
reply
562
views
Exact same results in Diffbind with different normalization methods
DiffBind
13 months ago
red_bricks
▴ 60
0
votes
1
reply
784
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
15 months ago
isaromero8888
• 0
0
votes
0
replies
785
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
15 months ago
Jawahar
• 0
0
votes
0
replies
455
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
15 months ago
frueher
• 0
0
votes
0
replies
434
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
15 months ago
Aswathy
• 0
0
votes
0
replies
620
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
15 months ago
Hai
• 0
0
votes
0
replies
543
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
16 months ago
inna.gur
• 0
0
votes
1
reply
1.4k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 16 months ago by
qq809825706
• 0 • written 20 months ago by
Mark
• 0
0
votes
2
replies
783
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 16 months ago by
Sam
▴ 10
1
vote
2
replies
659
views
Inconsistent results in DiffBind
DiffBind
16 months ago
Sam
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: CluserProfiler message "No gene can be mapped"
by
Carolina
• 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2
by
JKim
• 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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