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Views
Votes
Showing :
DiFFBind
•
reset
0
votes
1
reply
85
views
building samplesheet and plot profile
DiffBind
8 days ago • updated 6 days ago
yf
• 0
0
votes
5
replies
294
views
Diffbind interpretation of data - fold change
DiffBind
4 weeks ago
Vera
• 0
0
votes
0
replies
238
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
3 months ago
kim
• 0
0
votes
0
replies
182
views
diffbind covariates
DiffBind
ATACSeq
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
548
views
DiffBind dba.report discrepancy
DiffBind
3 months ago
aelbassiouny
• 0
0
votes
0
replies
128
views
DiffBind subset replicates
DiffBind
3 months ago
Haiping
• 0
0
votes
0
replies
232
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
4 months ago
Young Boqin
• 0
0
votes
0
replies
260
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
4 months ago
Alejandro
• 0
0
votes
2
replies
401
views
DiffBind for MBD-seq
MBD-seq
DiffBind
5 months ago
Marianna
▴ 20
0
votes
0
replies
295
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
5 months ago
Ian D.
▴ 70
0
votes
1
reply
340
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
5 months ago
mdidish
▴ 10
0
votes
0
replies
277
views
DiffBind dba.plotprofile y-axis range
DiffBind
5 months ago
Tara
• 0
0
votes
8
replies
818
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 6 months ago by
Rory Stark
★ 5.2k • written 6 months ago by
Marianna
▴ 20
1
vote
3
replies
555
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 6 months ago by
Rory Stark
★ 5.2k • written 6 months ago by
jesswhitts
• 0
0
votes
0
replies
426
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
7 months ago
gamma.jian
▴ 10
0
votes
2
replies
526
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
7 months ago
Mallory
• 0
0
votes
0
replies
296
views
Difference in Contrast in DiffBind
DiffBind
8 months ago
user_bioinfo
• 0
0
votes
0
replies
325
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
9 months ago
Dinesh
• 0
0
votes
1
reply
636
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 3 months ago by
B.N
• 0 • written 9 months ago by
Henry
▴ 10
0
votes
0
replies
427
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
9 months ago
yvonneh
• 0
0
votes
0
replies
317
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
9 months ago
Ian D.
▴ 70
0
votes
9
replies
1.4k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
9 months ago • updated 3 months ago
Ian D.
▴ 70
3
votes
1
reply
562
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 9 months ago by
Michael Love
43k • written 9 months ago by
marcusn
▴ 10
0
votes
1
reply
865
views
ATACseq merge peaks
DiffBind
updated 9 months ago by
ATpoint
★ 4.6k • written 9 months ago by
Shloka
• 0
0
votes
4
replies
609
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
9 months ago
lonn
• 0
0
votes
0
replies
326
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
9 months ago
Virangika
• 0
2
votes
2
replies
696
views
[DiffBind] Obtaining normalization factors
DiffBind
10 months ago • updated 9 months ago
Henry
▴ 10
2
votes
2
replies
1.1k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
10 months ago
Henry
▴ 10
0
votes
0
replies
416
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
10 months ago
feather-W
• 0
0
votes
0
replies
440
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
10 months ago
Ankit
▴ 20
0
votes
0
replies
386
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
10 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
413
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
10 months ago
erbrocato
• 0
0
votes
2
replies
669
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
11 months ago
Sam
▴ 10
0
votes
1
reply
505
views
Exact same results in Diffbind with different normalization methods
DiffBind
11 months ago • updated 10 months ago
red_bricks
▴ 60
0
votes
1
reply
688
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
12 months ago
isaromero8888
• 0
0
votes
0
replies
691
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
12 months ago
Jawahar
• 0
0
votes
0
replies
408
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
12 months ago
frueher
• 0
0
votes
0
replies
375
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
13 months ago
Aswathy
• 0
0
votes
0
replies
553
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
13 months ago
Hai
• 0
0
votes
0
replies
491
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
13 months ago
inna.gur
• 0
0
votes
1
reply
1.3k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 13 months ago by
qq809825706
• 0 • written 17 months ago by
Mark
• 0
0
votes
2
replies
698
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 14 months ago by
Sam
▴ 10
1
vote
2
replies
595
views
Inconsistent results in DiffBind
DiffBind
14 months ago
Sam
▴ 10
1
vote
1
reply
648
views
DiffBind getting Fold values of near 0
DiffBind
DESeq2
updated 14 months ago by
ATpoint
★ 4.6k • written 14 months ago by
Miquel
• 0
0
votes
0
replies
686
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
14 months ago
jared.andrews07
▴ 30
0
votes
0
replies
701
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
sophie.hfliu
• 0
2
votes
4
replies
1.6k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 16 months ago by
Matt Eldridge
▴ 10 • written 16 months ago by
r.murakami
• 0
2
votes
2
replies
719
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
16 months ago
r.murakami
• 0
1
vote
1
reply
840
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind
chipseq
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
lin.pei26
• 0
3
votes
7
replies
1.4k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 17 months ago by
Chris
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: error in ChAMP loading file
by
81becky
• 0
hi Giulia, it sounds like you're facing a frustating issue with your chAMP import. One common suggestion is to double-check your CSV fomat…
Answer: DESeq2 adujsted p-value cutoff seemingly not working
by
James W. MacDonald
68k
From `?results' ``` On p-values: By default, independent filtering is performed to select a set of genes for multiple tes…
Comment: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
by
SofieK
• 0
Thank you, I will try this and see.
Comment: DiffBind - question on the use of filtered or unfiltered input data
by
deltaexploitss
• 0
Data input is the adding of data into a computer. This can take place through an input device such as a keyboard. A user inputs data, which…
Comment: GenomeInfoDbData cannot install in R and warning had non-zero exit status
by
Renuka
• 0
how you did it pls explain
Votes
A: Effect of lfcThreshold on p-value in DESeq2
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
Answer: Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode =
Comment: Unused arguments error without used arguments in GSVA?
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