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Diffbind
•
reset
1
vote
10
replies
6.2k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 4 weeks ago by
nlp97204
• 0 • written 2.4 years ago by
Oscar
▴ 10
0
votes
0
replies
153
views
DiffBind plot.profile error
BiocParallel
DiffBind
3 months ago
this_is_me_trying
• 0
0
votes
0
replies
889
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
3 months ago
Muhammad
• 0
0
votes
0
replies
285
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
4 months ago
atlanta
• 0
0
votes
4
replies
2.2k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
4 months ago
Mengjun
• 0
0
votes
0
replies
176
views
DiffBind multi-tissue comparison
DiffBind
5 months ago
lryrainche
• 0
1
vote
8
replies
2.5k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
5 months ago • updated 4 months ago
Luca
• 0
0
votes
0
replies
285
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
6 months ago
Harish
• 0
0
votes
4
replies
1.3k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 6 months ago by
Harry
• 0 • written 6 months ago by
tifaGis
• 0
0
votes
1
reply
270
views
building samplesheet and plot profile
DiffBind
7 months ago
yf
• 0
0
votes
5
replies
670
views
Diffbind interpretation of data - fold change
DiffBind
7 months ago
Vera
• 0
0
votes
0
replies
502
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
10 months ago
kim
• 0
0
votes
0
replies
328
views
diffbind covariates
DiffBind
ATACSeq
updated 10 months ago by
Michael Love
43k • written 10 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
868
views
DiffBind dba.report discrepancy
DiffBind
10 months ago
aelbassiouny
• 0
0
votes
0
replies
268
views
DiffBind subset replicates
DiffBind
10 months ago
Haiping
• 0
0
votes
0
replies
509
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
10 months ago
Young Boqin
• 0
0
votes
0
replies
434
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
11 months ago
Alejandro
• 0
0
votes
2
replies
560
views
DiffBind for MBD-seq
MBD-seq
DiffBind
12 months ago
Marianna
▴ 20
0
votes
1
reply
654
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
12 months ago • updated 6 months ago
Ian D.
▴ 70
0
votes
1
reply
508
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
12 months ago
mdidish
▴ 10
0
votes
0
replies
432
views
DiffBind dba.plotprofile y-axis range
DiffBind
12 months ago
Tara
• 0
0
votes
8
replies
1.2k
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 13 months ago by
Rory Stark
★ 5.2k • written 13 months ago by
Marianna
▴ 20
1
vote
3
replies
831
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 13 months ago by
Rory Stark
★ 5.2k • written 13 months ago by
jesswhitts
• 0
0
votes
0
replies
634
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
14 months ago
gamma.jian
▴ 10
0
votes
2
replies
855
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
14 months ago
Mallory
• 0
0
votes
0
replies
458
views
Difference in Contrast in DiffBind
DiffBind
15 months ago
user_bioinfo
• 0
0
votes
0
replies
460
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
16 months ago
Dinesh
• 0
0
votes
1
reply
935
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 10 months ago by
B.N
• 0 • written 16 months ago by
Henry
▴ 10
0
votes
0
replies
665
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
16 months ago
yvonneh
• 0
0
votes
0
replies
432
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
16 months ago
Ian D.
▴ 70
0
votes
9
replies
1.7k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
16 months ago • updated 10 months ago
Ian D.
▴ 70
3
votes
1
reply
818
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 16 months ago by
Michael Love
43k • written 16 months ago by
marcusn
▴ 10
0
votes
1
reply
1.2k
views
ATACseq merge peaks
DiffBind
updated 16 months ago by
ATpoint
★ 4.9k • written 16 months ago by
Shloka
• 0
0
votes
4
replies
868
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
16 months ago
lonn
• 0
0
votes
0
replies
483
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
16 months ago
Virangika
• 0
2
votes
2
replies
973
views
[DiffBind] Obtaining normalization factors
DiffBind
16 months ago
Henry
▴ 10
2
votes
2
replies
1.6k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
16 months ago
Henry
▴ 10
0
votes
0
replies
547
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
17 months ago
feather-W
• 0
0
votes
0
replies
587
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
17 months ago
Ankit
▴ 20
0
votes
0
replies
550
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
17 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
537
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
17 months ago
erbrocato
• 0
0
votes
2
replies
836
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
17 months ago
Sam
▴ 10
0
votes
1
reply
673
views
Exact same results in Diffbind with different normalization methods
DiffBind
17 months ago
red_bricks
▴ 60
0
votes
1
reply
907
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
19 months ago
isaromero8888
• 0
0
votes
0
replies
889
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
19 months ago
Jawahar
• 0
0
votes
0
replies
535
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
19 months ago
frueher
• 0
0
votes
0
replies
505
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
19 months ago
Aswathy
• 0
0
votes
0
replies
736
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
20 months ago
Hai
• 0
0
votes
0
replies
623
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
20 months ago
inna.gur
• 0
2
votes
2
replies
1.9k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 4 months ago by
etiennedanis
• 0 • written 2.0 years ago by
Mark
▴ 10
678 results • Page
1 of 14
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0
by
littlefishes20
▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
snijesh
▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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