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diffbind
•
reset
0
votes
0
replies
35
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
2 days ago
Muhammad
• 0
1
vote
7
replies
3.3k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 10 days ago by
QFC
• 0 • written 2.1 years ago by
Oscar
▴ 10
0
votes
0
replies
167
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
4 weeks ago
atlanta
• 0
0
votes
4
replies
2.0k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
5 weeks ago • updated 27 days ago
Mengjun
• 0
0
votes
0
replies
76
views
DiffBind multi-tissue comparison
DiffBind
8 weeks ago
lryrainche
• 0
1
vote
8
replies
2.3k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
9 weeks ago • updated 5 weeks ago
Luca
• 0
0
votes
0
replies
144
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
10 weeks ago
Harish
• 0
0
votes
4
replies
1.2k
views
DiffBind edgeR normalization --- why are the normalization factors all equal to 1?
edgeR
DiffBind
updated 10 weeks ago by
Harry
• 0 • written 10 weeks ago by
tifaGis
• 0
0
votes
1
reply
179
views
building samplesheet and plot profile
DiffBind
3 months ago
yf
• 0
0
votes
5
replies
487
views
Diffbind interpretation of data - fold change
DiffBind
4 months ago
Vera
• 0
0
votes
0
replies
391
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
6 months ago
kim
• 0
0
votes
0
replies
264
views
diffbind covariates
DiffBind
ATACSeq
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
756
views
DiffBind dba.report discrepancy
DiffBind
6 months ago
aelbassiouny
• 0
0
votes
0
replies
187
views
DiffBind subset replicates
DiffBind
7 months ago
Haiping
• 0
0
votes
0
replies
380
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
7 months ago
Young Boqin
• 0
0
votes
0
replies
332
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
8 months ago
Alejandro
• 0
0
votes
2
replies
481
views
DiffBind for MBD-seq
MBD-seq
DiffBind
8 months ago
Marianna
▴ 20
0
votes
1
reply
557
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
8 months ago • updated 3 months ago
Ian D.
▴ 70
0
votes
1
reply
427
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
9 months ago
mdidish
▴ 10
0
votes
0
replies
353
views
DiffBind dba.plotprofile y-axis range
DiffBind
9 months ago
Tara
• 0
0
votes
8
replies
998
views
DiffBind full library size not reliable
DiffBind
Reads
MACS2
FullLibSize
updated 9 months ago by
Rory Stark
★ 5.2k • written 9 months ago by
Marianna
▴ 20
1
vote
3
replies
703
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 9 months ago by
Rory Stark
★ 5.2k • written 10 months ago by
jesswhitts
• 0
0
votes
0
replies
528
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
10 months ago
gamma.jian
▴ 10
0
votes
2
replies
701
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
11 months ago
Mallory
• 0
0
votes
0
replies
366
views
Difference in Contrast in DiffBind
DiffBind
12 months ago
user_bioinfo
• 0
0
votes
0
replies
384
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
12 months ago
Dinesh
• 0
0
votes
1
reply
795
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 6 months ago by
B.N
• 0 • written 12 months ago by
Henry
▴ 10
0
votes
0
replies
532
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
12 months ago
yvonneh
• 0
0
votes
0
replies
363
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
12 months ago
Ian D.
▴ 70
0
votes
9
replies
1.6k
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
12 months ago • updated 6 months ago
Ian D.
▴ 70
3
votes
1
reply
724
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 12 months ago by
Michael Love
43k • written 12 months ago by
marcusn
▴ 10
0
votes
1
reply
1.1k
views
ATACseq merge peaks
DiffBind
updated 12 months ago by
ATpoint
★ 4.8k • written 12 months ago by
Shloka
• 0
0
votes
4
replies
708
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
13 months ago
lonn
• 0
0
votes
0
replies
384
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
13 months ago
Virangika
• 0
2
votes
2
replies
845
views
[DiffBind] Obtaining normalization factors
DiffBind
13 months ago
Henry
▴ 10
2
votes
2
replies
1.4k
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
13 months ago
Henry
▴ 10
0
votes
0
replies
484
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
13 months ago
feather-W
• 0
0
votes
0
replies
509
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
13 months ago
Ankit
▴ 20
0
votes
0
replies
467
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
13 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
469
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
14 months ago
erbrocato
• 0
0
votes
2
replies
755
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
14 months ago
Sam
▴ 10
0
votes
1
reply
579
views
Exact same results in Diffbind with different normalization methods
DiffBind
14 months ago
red_bricks
▴ 60
0
votes
1
reply
799
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
15 months ago
isaromero8888
• 0
0
votes
0
replies
810
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
15 months ago
Jawahar
• 0
0
votes
0
replies
464
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
16 months ago
frueher
• 0
0
votes
0
replies
443
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
16 months ago
Aswathy
• 0
0
votes
0
replies
633
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
16 months ago
Hai
• 0
0
votes
0
replies
553
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
16 months ago
inna.gur
• 0
2
votes
2
replies
1.7k
views
DiffBind; Error: No sites have activity greater than filter value
DiffBind
updated 18 days ago by
etiennedanis
• 0 • written 20 months ago by
Mark
▴ 10
0
votes
2
replies
802
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 17 months ago by
Sam
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Answer: GSVA 1.52.2 (new API) nb of workers?
by
chaneymiller5908958
• 0
@[block blast][1] I'm running into the same issue with the parallelization. [1]: https://blockblastonline.com
Comment: Setting ylims in bam coverage plot and assigning compound sashimi numbers to ove
by
macdonaldfrench7286566
• 0
Regarding the ylim for the coverage [space waves][1], have you tried accessing the ylim slot of the CoverageTrack object after you've creat…
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an
by
Kateřina
• 0
I unfortunately haven't. Non-tidy grammar is fine, but I have wanted to use tidy-only grammar. Thank you nonetheless!
Comment: GAlignments Cigar to GRanges
by
pineiroalejandro
• 0
Wow, so easy! Thanks for your quick reply.
Comment: EuroBioC2023 abstract submission is open!
by
eilishhill8
• 0
Thanks for sharing this. I got it clearly now. Submit here: [https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/][1] [melon sa…
Votes
Answer: GAlignments Cigar to GRanges
Answer: GAlignments Cigar to GRanges
When running contrasts, does it use normalized read counts?
When running contrasts, does it use normalized read counts?
Importing Salmon counts with tximport with host and virus genomes
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