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Showing :
DiFFBind
•
reset
1
vote
11
replies
7.2k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.6 years ago by
Oscar
▴ 10
0
votes
0
replies
247
views
DiffBind plot.profile error
BiocParallel
DiffBind
6 months ago
this_is_me_trying
• 0
0
votes
0
replies
1.1k
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
6 months ago
Muhammad
• 0
0
votes
0
replies
350
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
7 months ago
atlanta
• 0
0
votes
4
replies
2.3k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
8 months ago • updated 7 months ago
Mengjun
• 0
0
votes
0
replies
253
views
DiffBind multi-tissue comparison
DiffBind
8 months ago
lryrainche
• 0
1
vote
8
replies
2.7k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
8 months ago • updated 7 months ago
Luca
• 0
0
votes
0
replies
365
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
9 months ago
Harish
• 0
0
votes
4
replies
1.4k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 9 months ago by
Harry
• 0 • written 9 months ago by
tifaGis
• 0
0
votes
1
reply
449
views
building samplesheet and plot profile
DiffBind
10 months ago
yf
• 0
0
votes
5
replies
834
views
Diffbind interpretation of data - fold change
DiffBind
11 months ago
Vera
• 0
0
votes
0
replies
592
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
13 months ago
kim
• 0
0
votes
0
replies
388
views
diffbind covariates
DiffBind
ATACSeq
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
975
views
DiffBind dba.report discrepancy
DiffBind
13 months ago
aelbassiouny
• 0
0
votes
0
replies
348
views
DiffBind subset replicates
DiffBind
13 months ago
Haiping
• 0
0
votes
0
replies
620
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
14 months ago
Young Boqin
• 0
0
votes
0
replies
510
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
14 months ago
Alejandro
• 0
0
votes
2
replies
633
views
DiffBind for MBD-seq
MBD-seq
DiffBind
15 months ago
Marianna
▴ 20
0
votes
1
reply
732
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
15 months ago • updated 9 months ago
Ian D.
▴ 70
0
votes
1
reply
622
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
15 months ago
mdidish
▴ 10
0
votes
0
replies
523
views
DiffBind dba.plotprofile y-axis range
DiffBind
15 months ago
Tara
• 0
0
votes
8
replies
1.4k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 16 months ago by
Rory Stark
★ 5.2k • written 16 months ago by
Marianna
▴ 20
1
vote
3
replies
920
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 16 months ago by
Rory Stark
★ 5.2k • written 16 months ago by
jesswhitts
• 0
0
votes
0
replies
809
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
17 months ago
gamma.jian
▴ 10
0
votes
2
replies
973
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
17 months ago
Mallory
• 0
0
votes
0
replies
516
views
Difference in Contrast in DiffBind
DiffBind
18 months ago
user_bioinfo
• 0
0
votes
0
replies
522
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
19 months ago
Dinesh
• 0
0
votes
1
reply
1.1k
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 13 months ago by
B.N
• 0 • written 19 months ago by
Henry
▴ 10
0
votes
0
replies
813
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
19 months ago
yvonneh
• 0
0
votes
0
replies
470
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
19 months ago
Ian D.
▴ 70
0
votes
9
replies
1.9k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
19 months ago • updated 13 months ago
Ian D.
▴ 70
3
votes
1
reply
888
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 19 months ago by
Michael Love
43k • written 19 months ago by
marcusn
▴ 10
0
votes
1
reply
1.3k
views
ATACseq merge peaks
DiffBind
updated 19 months ago by
ATpoint
★ 5.0k • written 19 months ago by
Shloka
• 0
0
votes
4
replies
961
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
19 months ago
lonn
• 0
0
votes
0
replies
537
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
19 months ago
Virangika
• 0
2
votes
2
replies
1.1k
views
[DiffBind] Obtaining normalization factors
DiffBind
20 months ago • updated 19 months ago
Henry
▴ 10
2
votes
2
replies
1.8k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
20 months ago
Henry
▴ 10
0
votes
0
replies
647
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
20 months ago
feather-W
• 0
0
votes
0
replies
638
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
20 months ago
Ankit
▴ 20
0
votes
0
replies
612
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
20 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
580
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
20 months ago
erbrocato
• 0
0
votes
2
replies
923
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
21 months ago
Sam
▴ 10
0
votes
1
reply
776
views
Exact same results in Diffbind with different normalization methods
DiffBind
21 months ago • updated 20 months ago
red_bricks
▴ 60
0
votes
1
reply
1.0k
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
22 months ago
isaromero8888
• 0
0
votes
0
replies
941
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
22 months ago
Jawahar
• 0
0
votes
0
replies
602
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
22 months ago
frueher
• 0
0
votes
0
replies
552
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
23 months ago
Aswathy
• 0
0
votes
0
replies
794
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
23 months ago
Hai
• 0
0
votes
0
replies
675
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
23 months ago
inna.gur
• 0
2
votes
2
replies
2.0k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 7 months ago by
etiennedanis
• 0 • written 2.3 years ago by
Mark
▴ 10
678 results • Page
1 of 14
Recent ...
Replies
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
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by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
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by
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53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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