Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
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
192
views
DiffBind plot.profile error
BiocParallel
DiffBind
4 months ago
this_is_me_trying
• 0
0
votes
0
replies
973
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
5 months ago
Muhammad
• 0
0
votes
0
replies
315
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
6 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
187
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
305
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
301
views
building samplesheet and plot profile
DiffBind
8 months ago
yf
• 0
0
votes
5
replies
742
views
Diffbind interpretation of data - fold change
DiffBind
9 months ago
Vera
• 0
0
votes
0
replies
529
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
11 months ago
kim
• 0
0
votes
0
replies
346
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
895
views
DiffBind dba.report discrepancy
DiffBind
11 months ago
aelbassiouny
• 0
0
votes
0
replies
298
views
DiffBind subset replicates
DiffBind
12 months ago
Haiping
• 0
0
votes
0
replies
545
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
12 months ago
Young Boqin
• 0
0
votes
0
replies
458
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
13 months ago
Alejandro
• 0
0
votes
2
replies
595
views
DiffBind for MBD-seq
MBD-seq
DiffBind
13 months ago
Marianna
▴ 20
0
votes
1
reply
682
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
13 months ago • updated 8 months ago
Ian D.
▴ 70
0
votes
1
reply
549
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
14 months ago
mdidish
▴ 10
0
votes
0
replies
450
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
868
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 14 months ago by
Rory Stark
★ 5.2k • written 15 months ago by
jesswhitts
• 0
0
votes
0
replies
667
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
15 months ago
gamma.jian
▴ 10
0
votes
2
replies
892
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
16 months ago
Mallory
• 0
0
votes
0
replies
476
views
Difference in Contrast in DiffBind
DiffBind
17 months ago
user_bioinfo
• 0
0
votes
0
replies
488
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
17 months ago
Dinesh
• 0
0
votes
1
reply
989
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
723
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
17 months ago
yvonneh
• 0
0
votes
0
replies
443
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
842
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
912
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
18 months ago
lonn
• 0
0
votes
0
replies
504
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
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
558
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
18 months ago
feather-W
• 0
0
votes
0
replies
610
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
18 months ago
Ankit
▴ 20
0
votes
0
replies
568
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
18 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
550
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
19 months ago
erbrocato
• 0
0
votes
2
replies
858
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
19 months ago
Sam
▴ 10
0
votes
1
reply
697
views
Exact same results in Diffbind with different normalization methods
DiffBind
19 months ago
red_bricks
▴ 60
0
votes
1
reply
958
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
909
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
21 months ago
Jawahar
• 0
0
votes
0
replies
562
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
21 months ago
frueher
• 0
0
votes
0
replies
522
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
21 months ago
Aswathy
• 0
0
votes
0
replies
764
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
21 months ago
Hai
• 0
0
votes
0
replies
645
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: 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…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: 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
Awards
• All
Popular Question
to
Michael Love
43k
Popular Question
to
Peter
• 0
Popular Question
to
Travis
• 0
Popular Question
to
James W. MacDonald
68k
Popular Question
to
Gordon Smyth
53k
Locations
• All
United States,
20 minutes ago
The city by the bay,
1 hour ago
Hong Kong,
4 hours ago
WEHI, Melbourne, Australia,
4 hours ago
Pittsburgh, United States,
7 hours ago
Traffic: 1385 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6