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diffBind
•
reset
1
vote
11
replies
6.7k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.5 years ago by
Oscar
▴ 10
0
votes
0
replies
185
views
DiffBind plot.profile error
BiocParallel
DiffBind
4 months ago
this_is_me_trying
• 0
0
votes
0
replies
959
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
4 months ago
Muhammad
• 0
0
votes
0
replies
309
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
5 months ago
atlanta
• 0
0
votes
4
replies
2.3k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
6 months ago • updated 5 months ago
Mengjun
• 0
0
votes
0
replies
185
views
DiffBind multi-tissue comparison
DiffBind
6 months ago
lryrainche
• 0
1
vote
8
replies
2.6k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
7 months ago • updated 6 months ago
Luca
• 0
0
votes
0
replies
303
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
7 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 7 months ago by
Harry
• 0 • written 7 months ago by
tifaGis
• 0
0
votes
1
reply
298
views
building samplesheet and plot profile
DiffBind
8 months ago
yf
• 0
0
votes
5
replies
739
views
Diffbind interpretation of data - fold change
DiffBind
9 months ago
Vera
• 0
0
votes
0
replies
524
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
11 months ago
kim
• 0
0
votes
0
replies
345
views
diffbind covariates
DiffBind
ATACSeq
updated 11 months ago by
Michael Love
43k • written 11 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
892
views
DiffBind dba.report discrepancy
DiffBind
11 months ago
aelbassiouny
• 0
0
votes
0
replies
296
views
DiffBind subset replicates
DiffBind
11 months ago
Haiping
• 0
0
votes
0
replies
537
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
12 months ago
Young Boqin
• 0
0
votes
0
replies
455
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
12 months ago
Alejandro
• 0
0
votes
2
replies
588
views
DiffBind for MBD-seq
MBD-seq
DiffBind
13 months ago
Marianna
▴ 20
0
votes
1
reply
677
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
13 months ago • updated 7 months ago
Ian D.
▴ 70
0
votes
1
reply
543
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
14 months ago
mdidish
▴ 10
0
votes
0
replies
448
views
DiffBind dba.plotprofile y-axis range
DiffBind
14 months ago
Tara
• 0
0
votes
8
replies
1.3k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 14 months ago by
Rory Stark
★ 5.2k • written 14 months ago by
Marianna
▴ 20
1
vote
3
replies
865
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 14 months ago by
Rory Stark
★ 5.2k • written 14 months ago by
jesswhitts
• 0
0
votes
0
replies
663
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
15 months ago
gamma.jian
▴ 10
0
votes
2
replies
890
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
15 months ago
Mallory
• 0
0
votes
0
replies
472
views
Difference in Contrast in DiffBind
DiffBind
17 months ago
user_bioinfo
• 0
0
votes
0
replies
484
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
17 months ago
Dinesh
• 0
0
votes
1
reply
982
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 11 months ago by
B.N
• 0 • written 17 months ago by
Henry
▴ 10
0
votes
0
replies
716
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
17 months ago
yvonneh
• 0
0
votes
0
replies
441
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
17 months ago
Ian D.
▴ 70
0
votes
9
replies
1.8k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
17 months ago • updated 11 months ago
Ian D.
▴ 70
3
votes
1
reply
840
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 17 months ago by
Michael Love
43k • written 17 months ago by
marcusn
▴ 10
0
votes
1
reply
1.3k
views
ATACseq merge peaks
DiffBind
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
Shloka
• 0
0
votes
4
replies
909
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
17 months ago
lonn
• 0
0
votes
0
replies
499
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
18 months ago
Virangika
• 0
2
votes
2
replies
1.0k
views
[DiffBind] Obtaining normalization factors
DiffBind
18 months ago • updated 17 months ago
Henry
▴ 10
2
votes
2
replies
1.7k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
18 months ago
Henry
▴ 10
0
votes
0
replies
556
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
18 months ago
feather-W
• 0
0
votes
0
replies
605
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
18 months ago
Ankit
▴ 20
0
votes
0
replies
565
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
18 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
547
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
18 months ago
erbrocato
• 0
0
votes
2
replies
852
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
19 months ago
Sam
▴ 10
0
votes
1
reply
693
views
Exact same results in Diffbind with different normalization methods
DiffBind
19 months ago
red_bricks
▴ 60
0
votes
1
reply
951
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
20 months ago
isaromero8888
• 0
0
votes
0
replies
907
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
20 months ago
Jawahar
• 0
0
votes
0
replies
557
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
20 months ago
frueher
• 0
0
votes
0
replies
521
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
21 months ago
Aswathy
• 0
0
votes
0
replies
761
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
21 months ago
Hai
• 0
0
votes
0
replies
640
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
21 months ago
inna.gur
• 0
2
votes
2
replies
1.9k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 5 months ago by
etiennedanis
• 0 • written 2.1 years ago by
Mark
▴ 10
678 results • Page
1 of 14
Recent ...
Replies
Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Results with PON give more variants
by
ejafgdf4.ge.r.m
• 0
It s common to expect Mutect2 with a PON to be a strict subset of Mutect2 without it but seeing unique variants in Mutect2withPON isn t unu…
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package
by
ksankaran
• 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Comment: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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