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DiffBind
•
reset
0
votes
1
reply
260
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
updated 3 days ago by
ATpoint
★ 4.8k • written 3 days ago by
Mengjun
• 0
0
votes
0
replies
48
views
DiffBind multi-tissue comparison
DiffBind
23 days ago
lryrainche
• 0
1
vote
8
replies
2.1k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw
ChIPseq
DESeq2
DiffBind
29 days ago • updated 20 hours ago
Luca
• 0
0
votes
7
replies
2.5k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
updated 4 weeks ago by
robert
• 0 • written 24 months ago by
Oscar
• 0
0
votes
0
replies
111
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
5 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 5 weeks ago by
Harry
• 0 • written 5 weeks ago by
tifaGis
• 0
0
votes
1
reply
152
views
building samplesheet and plot profile
DiffBind
10 weeks ago • updated 9 weeks ago
yf
• 0
0
votes
5
replies
425
views
Diffbind interpretation of data - fold change
DiffBind
3 months ago
Vera
• 0
0
votes
0
replies
321
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
5 months ago
kim
• 0
0
votes
0
replies
233
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
688
views
DiffBind dba.report discrepancy
DiffBind
5 months ago
aelbassiouny
• 0
0
votes
0
replies
161
views
DiffBind subset replicates
DiffBind
5 months ago
Haiping
• 0
0
votes
0
replies
333
views
Background normalization of Diffbind dba.normalize
Normalization
DiffBind
6 months ago
Young Boqin
• 0
0
votes
0
replies
306
views
Trying to understand basic DiffBind usage
ChIPSeq
DiffBind
6 months ago
Alejandro
• 0
0
votes
2
replies
461
views
DiffBind for MBD-seq
MBD-seq
DiffBind
7 months ago
Marianna
▴ 20
0
votes
1
reply
524
views
DiffBind - observation that the default union overlap is actually a gap of 1 bp
DiffBind
7 months ago • updated 8 weeks ago
Ian D.
▴ 70
0
votes
1
reply
394
views
DiffBind remove Unplace Chromosome (chrUn)
DiffBind
8 months ago • updated 7 months ago
mdidish
▴ 10
0
votes
0
replies
329
views
DiffBind dba.plotprofile y-axis range
DiffBind
8 months ago
Tara
• 0
0
votes
8
replies
945
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
653
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
494
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
9 months ago
gamma.jian
▴ 10
0
votes
2
replies
637
views
Trouble reading samplesheet in with diffbind to create dba
DiffBind
DifferentialPeakCalling
9 months ago
Mallory
• 0
0
votes
0
replies
340
views
Difference in Contrast in DiffBind
DiffBind
11 months ago
user_bioinfo
• 0
0
votes
0
replies
361
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 months ago
Dinesh
• 0
0
votes
1
reply
741
views
dba.plotProfile() plotting and interpretation
DiffBind
updated 5 months ago by
B.N
• 0 • written 11 months ago by
Henry
▴ 10
0
votes
0
replies
500
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
11 months ago
yvonneh
• 0
0
votes
0
replies
347
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
678
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
679
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
362
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
11 months ago
Virangika
• 0
2
votes
2
replies
799
views
[DiffBind] Obtaining normalization factors
DiffBind
12 months ago • updated 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
12 months ago
Henry
▴ 10
0
votes
0
replies
466
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
436
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
730
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
13 months ago
Sam
▴ 10
0
votes
1
reply
551
views
Exact same results in Diffbind with different normalization methods
DiffBind
13 months ago • updated 12 months ago
red_bricks
▴ 60
0
votes
1
reply
766
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
765
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
444
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl
ChIPSeq
DiffBind
14 months ago
frueher
• 0
0
votes
0
replies
427
views
Errror in running EdgeR based differential analysis in diffbind
DiffBind
15 months ago
Aswathy
• 0
0
votes
0
replies
601
views
Differential Binding of CUT&Tag peaks with normalization using scaling factor
DiffBind
CUT&Tag
15 months ago
Hai
• 0
0
votes
0
replies
525
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
763
views
In DiffBind, dba.blacklist changes the minOverlap parameter
DiffBind
written 16 months ago by
Sam
▴ 10
1
vote
2
replies
646
views
Inconsistent results in DiffBind
DiffBind
16 months ago
Sam
▴ 10
1
vote
1
reply
692
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
50 results • Page
1 of 1
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Answer: fast apply on RleList
by
James W. MacDonald
68k
There is already a 'mean' function that will dispatch on an `RleList` that you can use. I don't have a long `RleList` in hand to test it on…
Answer: Custom CDF creation for HTA 2.0 array using GTF annotation
by
James W. MacDonald
68k
It doesn't appear that Manhong Dai is working at UM any longer, and the webpage appears to have fallen into disrepair (for example, the lin…
Comment: how to use `arrayWeightsQuick()`?
by
matthew
• 0
In the specific use-case I have in mind, `expression` is a simple `matrix` of log2 gene expression per sample, no missing values.
Comment: BiocParallel_1.40.1.tar.gz not available
by
Johan
• 0
It worked. Thanks :)
Comment: Model performance for spline modelling of RNA-seq timecourses in edgeR
by
skiaphrene
▴ 10
Dear Gordon, Thank you very much for your prompt reply. I agree with the limma/edgeR perspective of including all potentially explanatory…
Votes
Answer: BiocParallel_1.40.1.tar.gz not available
Modelling gene program dynamics across time with {lemur}
A: DESeq2 one group vs multiple groups comparison in presence of batch effect
Comment: BiocParallel_1.40.1.tar.gz not available
Comment: BiocParallel_1.40.1.tar.gz not available
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