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diffBind
•
reset
0
votes
1
reply
247
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
updated 1 day ago by
ATpoint
★ 4.8k • written 1 day ago by
Mengjun
• 0
0
votes
0
replies
47
views
DiffBind multi-tissue comparison
DiffBind
22 days ago
lryrainche
• 0
1
vote
6
replies
1.7k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
28 days ago • updated 10 hours ago
Luca
• 0
0
votes
7
replies
2.5k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 4 weeks ago by
robert
• 0 • written 23 months ago by
Oscar
• 0
0
votes
0
replies
109
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
5 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 4 weeks ago by
Harry
• 0 • written 5 weeks ago by
tifaGis
• 0
0
votes
1
reply
149
views
building samplesheet and plot profile
DiffBind
9 weeks ago
yf
• 0
0
votes
5
replies
421
views
Diffbind interpretation of data - fold change
DiffBind
3 months ago
Vera
• 0
0
votes
0
replies
321
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
5 months ago
kim
• 0
0
votes
0
replies
232
views
diffbind covariates
DiffBind
ATACSeq
updated 5 months ago by
Michael Love
43k • written 5 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
687
views
DiffBind dba.report discrepancy
DiffBind
5 months ago
aelbassiouny
• 0
0
votes
0
replies
160
views
DiffBind subset replicates
DiffBind
5 months ago
Haiping
• 0
0
votes
0
replies
332
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
6 months ago
Young Boqin
• 0
0
votes
0
replies
306
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
6 months ago
Alejandro
• 0
0
votes
2
replies
458
views
DiffBind for MBD-seq
MBD-seq
DiffBind
7 months ago
Marianna
▴ 20
0
votes
1
reply
524
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
7 months ago • updated 8 weeks ago
Ian D.
▴ 70
0
votes
1
reply
393
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
7 months ago
mdidish
▴ 10
0
votes
0
replies
326
views
DiffBind dba.plotprofile y-axis range
DiffBind
7 months ago
Tara
• 0
0
votes
8
replies
943
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
643
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 8 months ago by
Rory Stark
★ 5.2k • written 8 months ago by
jesswhitts
• 0
0
votes
0
replies
492
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
9 months ago
gamma.jian
▴ 10
0
votes
2
replies
636
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
9 months ago
Mallory
• 0
0
votes
0
replies
339
views
Difference in Contrast in DiffBind
DiffBind
10 months ago
user_bioinfo
• 0
0
votes
0
replies
360
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 months ago
Dinesh
• 0
0
votes
1
reply
740
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
498
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
11 months ago
yvonneh
• 0
0
votes
0
replies
345
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 5 months ago
Ian D.
▴ 70
3
votes
1
reply
677
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
1.0k
views
ATACseq merge peaks
DiffBind
updated 11 months ago by
ATpoint
★ 4.8k • written 11 months ago by
Shloka
• 0
0
votes
4
replies
679
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
11 months ago
lonn
• 0
0
votes
0
replies
361
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
11 months ago
Virangika
• 0
2
votes
2
replies
795
views
[DiffBind] Obtaining normalization factors
DiffBind
12 months ago • updated 11 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
464
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
12 months ago
feather-W
• 0
0
votes
0
replies
483
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
12 months ago
Ankit
▴ 20
0
votes
0
replies
436
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
12 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
447
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
12 months ago
erbrocato
• 0
0
votes
2
replies
730
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
13 months ago
Sam
▴ 10
0
votes
1
reply
551
views
Exact same results in Diffbind with different normalization methods
DiffBind
13 months ago • updated 12 months ago
red_bricks
▴ 60
0
votes
1
reply
765
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
14 months ago
isaromero8888
• 0
0
votes
0
replies
764
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
14 months ago
Jawahar
• 0
0
votes
0
replies
441
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
14 months ago
frueher
• 0
0
votes
0
replies
426
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
15 months ago
Aswathy
• 0
0
votes
0
replies
601
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
15 months ago
Hai
• 0
0
votes
0
replies
523
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
15 months ago
inna.gur
• 0
0
votes
1
reply
1.4k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 15 months ago by
qq809825706
• 0 • written 19 months ago by
Mark
• 0
0
votes
2
replies
763
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 16 months ago by
Sam
▴ 10
1
vote
2
replies
646
views
Inconsistent results in DiffBind
DiffBind
16 months ago
Sam
▴ 10
1
vote
1
reply
690
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 16 months ago by
ATpoint
★ 4.8k • written 16 months ago by
Miquel
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR
by
Gordon Smyth
52k
I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly?
by
James W. MacDonald
68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Answer: Origin of the labels for the SingleCellMultiModal dataset
by
ATpoint
★ 4.8k
If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…
Votes
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
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