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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
199
views
DiffBind plot.profile error
BiocParallel
DiffBind
4 months ago
this_is_me_trying
• 0
0
votes
0
replies
984
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
323
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
Mengjun
• 0
0
votes
0
replies
193
views
DiffBind multi-tissue comparison
DiffBind
7 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
311
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
310
views
building samplesheet and plot profile
DiffBind
8 months ago
yf
• 0
0
votes
5
replies
768
views
Diffbind interpretation of data - fold change
DiffBind
9 months ago
Vera
• 0
0
votes
0
replies
537
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
11 months ago
kim
• 0
0
votes
0
replies
351
views
diffbind covariates
DiffBind
ATACSeq
updated 12 months ago by
Michael Love
43k • written 12 months ago by
Alpesh Querer
▴ 220
0
votes
2
replies
906
views
DiffBind dba.report discrepancy
DiffBind
12 months ago
aelbassiouny
• 0
0
votes
0
replies
303
views
DiffBind subset replicates
DiffBind
12 months ago
Haiping
• 0
0
votes
0
replies
559
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
12 months ago
Young Boqin
• 0
0
votes
0
replies
466
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
13 months ago
Alejandro
• 0
0
votes
2
replies
601
views
DiffBind for MBD-seq
MBD-seq
DiffBind
14 months ago
Marianna
▴ 20
0
votes
1
reply
689
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
14 months ago • updated 8 months ago
Ian D.
▴ 70
0
votes
1
reply
560
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
14 months ago
mdidish
▴ 10
0
votes
0
replies
464
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
877
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 15 months ago by
Rory Stark
★ 5.2k • written 15 months ago by
jesswhitts
• 0
0
votes
0
replies
685
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
16 months ago
gamma.jian
▴ 10
0
votes
2
replies
901
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
16 months ago
Mallory
• 0
0
votes
0
replies
482
views
Difference in Contrast in DiffBind
DiffBind
17 months ago
user_bioinfo
• 0
0
votes
0
replies
493
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
17 months ago
Dinesh
• 0
0
votes
1
reply
1.0k
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
736
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
17 months ago
yvonneh
• 0
0
votes
0
replies
449
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
18 months ago • updated 12 months ago
Ian D.
▴ 70
3
votes
1
reply
849
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 months ago by
marcusn
▴ 10
0
votes
1
reply
1.3k
views
ATACseq merge peaks
DiffBind
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
Shloka
• 0
0
votes
4
replies
919
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
507
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
563
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
19 months ago
feather-W
• 0
0
votes
0
replies
613
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
19 months ago
Ankit
▴ 20
0
votes
0
replies
579
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
19 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
558
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
19 months ago
erbrocato
• 0
0
votes
2
replies
878
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
19 months ago
Sam
▴ 10
0
votes
1
reply
715
views
Exact same results in Diffbind with different normalization methods
DiffBind
19 months ago
red_bricks
▴ 60
0
votes
1
reply
969
views
Extracting binding matrix with raw counts from DiffBind in ATAC-seq data not working
DiffBind
ATACSeq
21 months ago
isaromero8888
• 0
0
votes
0
replies
915
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
570
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
21 months ago
frueher
• 0
0
votes
0
replies
527
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
21 months ago
Aswathy
• 0
0
votes
0
replies
767
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
22 months ago
Hai
• 0
0
votes
0
replies
653
views
ATACseq- Counts around TSS plot
DiffBind
ATACSeq
22 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 2.2 years ago by
Mark
▴ 10
678 results • Page
1 of 14
Recent ...
Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry
by
teamardigen
• 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Votes
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
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