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DiFFBind
•
reset
0
votes
0
replies
42
views
DiffBind multi-tissue comparison
DiffBind
17 days ago
lryrainche
• 0
1
vote
2
replies
1.2k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
23 days ago • updated 22 days ago
Luca
• 0
0
votes
7
replies
2.4k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 29 days ago by
robert
• 0 • written 23 months ago by
Oscar
• 0
0
votes
0
replies
99
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
4 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
145
views
building samplesheet and plot profile
DiffBind
9 weeks ago • updated 8 weeks ago
yf
• 0
0
votes
5
replies
395
views
Diffbind interpretation of data - fold change
DiffBind
12 weeks ago
Vera
• 0
0
votes
0
replies
312
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
5 months ago
kim
• 0
0
votes
0
replies
230
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
679
views
DiffBind dba.report discrepancy
DiffBind
5 months ago
aelbassiouny
• 0
0
votes
0
replies
159
views
DiffBind subset replicates
DiffBind
5 months ago
Haiping
• 0
0
votes
0
replies
331
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
5 months ago
Young Boqin
• 0
0
votes
0
replies
302
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
6 months ago
Alejandro
• 0
0
votes
2
replies
454
views
DiffBind for MBD-seq
MBD-seq
DiffBind
7 months ago
Marianna
▴ 20
0
votes
1
reply
517
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
7 months ago • updated 7 weeks ago
Ian D.
▴ 70
0
votes
1
reply
391
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
7 months ago
mdidish
▴ 10
0
votes
0
replies
325
views
DiffBind dba.plotprofile y-axis range
DiffBind
7 months ago
Tara
• 0
0
votes
8
replies
930
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
633
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
625
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
9 months ago
Mallory
• 0
0
votes
0
replies
338
views
Difference in Contrast in DiffBind
DiffBind
10 months ago
user_bioinfo
• 0
0
votes
0
replies
358
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 months ago
Dinesh
• 0
0
votes
1
reply
732
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 4 months ago by
B.N
• 0 • written 11 months ago by
Henry
▴ 10
0
votes
0
replies
494
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
11 months ago
yvonneh
• 0
0
votes
0
replies
344
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
676
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
675
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
789
views
[DiffBind] Obtaining normalization factors
DiffBind
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
11 months ago
Henry
▴ 10
0
votes
0
replies
462
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
434
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
725
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
12 months ago
Sam
▴ 10
0
votes
1
reply
547
views
Exact same results in Diffbind with different normalization methods
DiffBind
12 months ago
red_bricks
▴ 60
0
votes
1
reply
761
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
761
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
439
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
14 months ago
frueher
• 0
0
votes
0
replies
424
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
14 months ago
Aswathy
• 0
0
votes
0
replies
597
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
15 months ago
Hai
• 0
0
votes
0
replies
521
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
761
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 16 months ago by
Sam
▴ 10
1
vote
2
replies
639
views
Inconsistent results in DiffBind
DiffBind
16 months ago • updated 15 months ago
Sam
▴ 10
1
vote
1
reply
689
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
0
votes
0
replies
749
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw
ChIPseq
DiffBind
16 months ago
jared.andrews07
▴ 30
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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