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Showing :
diffbind
•
reset
1
vote
16
replies
3.6k
views
Error: could not find function "dba"
software error
diffbind
dba
7.5 years ago
mmarins
• 0
0
votes
14
replies
2.4k
views
got 0 significant differential bound (DB)
diffbind
6.9 years ago
mforoo1
• 0
0
votes
7
replies
1.9k
views
DiffBind:Treatments + second factor
DiffBind
diffbind
updated 9.5 years ago by
Rory Stark
★ 5.2k • written 9.5 years ago by
sergio.espeso-gil
• 0
16
votes
9
replies
6.5k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 6.5 years ago by
Rory Stark
★ 5.2k • written 8.1 years ago by
florian.noack
▴ 60
3
votes
6
replies
4.4k
views
Analyzing data without replicates using DiffBind
diffbind
bioconductor
differential binding analysis
without replicate
chipseq
6.5 years ago
Hesh
▴ 10
0
votes
9
replies
2.7k
views
Questions about DiffBind loaded peaks and re-count reads
DiffBind
3.4 years ago • updated 2.2 years ago
Tongjun
• 0
0
votes
6
replies
1.5k
views
DiffBind error with dba.count
diffbind
updated 6.0 years ago by
Rory Stark
★ 5.2k • written 6.1 years ago by
hhhcce
• 0
6
votes
8
replies
2.5k
views
Interaction with DESeq2 via DiffBind
diffbind
deseq2
interactions
updated 3.4 years ago by
pierre.marin
• 0 • written 6.5 years ago by
rbronste
▴ 60
1
vote
6
replies
5.8k
views
question about DiffBind
DiffBind
differential binding analysis
updated 8.7 years ago by
Rory Stark
★ 5.2k • written 8.7 years ago by
February
• 0
3
votes
5
replies
2.5k
views
Work with GRanges objects in DiffBind
diffbind
updated 7.8 years ago by
termanini
▴ 10 • written 8.7 years ago by
xulong.wang
• 0
1
vote
6
replies
2.6k
views
Diffbind EdgeR and DESeq2 normalization
diffbind
normalized counts
7.8 years ago
GFM
▴ 20
2
votes
6
replies
2.3k
views
SICER and Diffbind
Sicer
diffbind
9.1 years ago
sergio.espeso-gil
• 0
0
votes
4
replies
1.4k
views
DiffBind: Report differential sites by fold > & < 0
diffbind
updated 9.5 years ago by
Rory Stark
★ 5.2k • written 9.5 years ago by
sergio.espeso-gil
• 0
2
votes
4
replies
835
views
Extracting origin info from DB sites
DiffBind
updated 6.2 years ago by
Rory Stark
★ 5.2k • written 6.2 years ago by
michal.inbar
• 0
0
votes
6
replies
3.0k
views
DiffBind: Error in heights * sapply(called, function(x) x)
diffbind
dba.count
summits
updated 3.3 years ago by
Rory Stark
★ 5.2k • written 6.4 years ago by
zhaolin20042008
• 0
2
votes
7
replies
1.3k
views
Deferentially binding site is the same for all the samples
chip-seq
diffBind
sequence_analysis
updated 3.8 years ago by
Rory Stark
★ 5.2k • written 3.8 years ago by
Mar Mar
▴ 20
4
votes
11
replies
3.3k
views
How to get all possible comparisons in DiffBind
diffbind
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 5.3 years ago by
bony.dekumar
▴ 10
0
votes
4
replies
2.6k
views
Diffbind - Problem with calling plotting functions after analysis "contrasts greater than the number of contrasts"
Diffbind
9.6 years ago
ben
• 0
1
vote
4
replies
1.3k
views
DiifBind version difference
diffbind
new version
updated 8.9 years ago by
Rory Stark
★ 5.2k • written 9.0 years ago by
pkra
• 0
0
votes
4
replies
1.8k
views
How to set the parameter "fragmentSize" in DiffBind and set parameter for paired-end CHIP-seq data?
diffbind
software error
updated 6.8 years ago by
Rory Stark
★ 5.2k • written 6.8 years ago by
xieyongjun93
• 0
1
vote
4
replies
2.0k
views
MAnorm output as DiffBind input.
MAnorm
diffbind
normalization
chipseq
updated 3.5 years ago by
Rory Stark
★ 5.2k • written 6.3 years ago by
ajeet
• 0
0
votes
4
replies
1.7k
views
consensus analysis and dba.count function
diffbind
consensus
7.3 years ago
pabla86
• 0
1
vote
5
replies
4.7k
views
DiffBind error
Alignment
DiffBind
Alignment
DiffBind
updated 11.3 years ago by
Rory Stark
★ 5.2k • written 11.3 years ago by
José Luis Lavín
▴ 280
0
votes
4
replies
2.3k
views
Error with Diffbind
diffbind
updated 8.7 years ago by
Rory Stark
★ 5.2k • written 8.7 years ago by
bdk
• 0
2
votes
4
replies
2.1k
views
Normalizing Cut&Tag peak data
Normalization
Peakdata
DiffBind
Cut&Tag
updated 19 months ago by
ATpoint
★ 4.1k • written 19 months ago by
bhandary.8590
▴ 20
4
votes
8
replies
2.2k
views
ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind
ChIPQC
8.3 years ago
JD
▴ 10
0
votes
8
replies
4.5k
views
DiffBind - Error in dba.count() when passing mask or peaks
diffbind
updated 8.0 years ago by
kmavrommatis
• 0 • written 8.2 years ago by
gaia.zaffaroni
• 0
1
vote
7
replies
1.4k
views
Conc_1 in differnet dba.report result is slightly different
DiffBind
updated 3.3 years ago by
Rory Stark
★ 5.2k • written 3.3 years ago by
Guandong Shang
▴ 40
0
votes
7
replies
1.1k
views
Issue in generating a new DBA object with custom counts
DiffBind
dbaobject
16 months ago • updated 15 months ago
francesco.gandolfi
• 0
0
votes
5
replies
1.5k
views
Change DiffBind correlation matrix scale
diffbind
scale
correlation matrix
8.5 years ago
eli7javasky
• 0
5
votes
7
replies
3.5k
views
What does dba.PCA in DiffBind exactly do?
diffbind
pca
updated 2.7 years ago by
Rory Stark
★ 5.2k • written 8.5 years ago by
renanec
▴ 20
0
votes
5
replies
2.1k
views
error loading dba in DiffBind
DiffBind
DiffBind
updated 10.9 years ago by
Lawson, Nathan
▴ 30 • written 10.9 years ago by
Gord Brown
▴ 650
5
votes
10
replies
1.8k
views
Learning DiffBind - some basic questions
DiffBind
updated 3.1 years ago by
Rory Stark
★ 5.2k • written 3.4 years ago by
Sam
▴ 10
3
votes
4
replies
2.4k
views
How to get the list of genes from DiffBind dba.report or dba.peakset
diffbind
updated 2.6 years ago by
mdidish
▴ 10 • written 5.8 years ago by
Bordiya
▴ 10
2
votes
6
replies
4.2k
views
DiffBind installation doesn't work
diffbind
go.db
8.9 years ago • updated 8.8 years ago
Gary
▴ 20
0
votes
6
replies
1.4k
views
Unexpected results in the dba.report output files
diffbind
updated 6.3 years ago by
ck15115
• 0 • written 6.5 years ago by
Silvia
• 0
0
votes
4
replies
1.1k
views
Plotting the peak counts for filtering
diffbind
updated 9.0 years ago by
Rory Stark
★ 5.2k • written 9.0 years ago by
mc.suciu
• 0
1
vote
4
replies
2.2k
views
DiffBind not accessible files in Example data
diffbind
updated 3.0 years ago by
Rory Stark
★ 5.2k • written 6.4 years ago by
bobfukkink
• 0
3
votes
12
replies
3.4k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 2.7 years ago by
Rory Stark
★ 5.2k • written 4.6 years ago by
zhenfeng.liu1
▴ 20
1
vote
16
replies
4.8k
views
DiffBind Batch Effect
diffbind
atac
6.9 years ago
niu.shengyong
• 0
5
votes
17
replies
1.8k
views
DiffBind : More fragment sizes than libraries
diffbind
updated 6.9 years ago by
Rory Stark
★ 5.2k • written 6.9 years ago by
ZheFrench
▴ 50
4
votes
7
replies
2.5k
views
Diffbind dba.analyze Error in d$span : $ operator is invalid for atomic vectors
diffbind
updated 14 months ago by
xzpgocxx
• 0 • written 9.1 years ago by
danishm20
▴ 10
0
votes
5
replies
1.9k
views
ChIPseq diffbind merging peaks
diffbind
merging_peaks
7.2 years ago
veronique.storme
• 0
1
vote
8
replies
1.9k
views
Global reduction of epigenetic factors (regularized log transformation DESeq2) ~ Diffbind
deseq2
diffbind
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
JunLVI
▴ 40
2
votes
6
replies
3.4k
views
DiffBind: reading in peaksets generated by Homer2
diffbind
updated 9.0 years ago by
sergio.espeso-gil
• 0 • written 9.3 years ago by
iliya.lefterov
▴ 10
0
votes
3
replies
1.5k
views
DiffBind EdgeR vs DeSeq2 diff peak counts
diffbind
7.3 years ago
rbronste
▴ 60
4
votes
5
replies
1.8k
views
Multi-factor blocking in DiffBind
diffbind
differential binding analysis
multiple factor design
written 6.6 years ago by
jared.andrews07
▴ 30
0
votes
3
replies
1.5k
views
Change color of Diffbind's PCA and clustered heatmap plot()
DiffBind
plot
color
updated 4.3 years ago by
Rory Stark
★ 5.2k • written 4.5 years ago by
melnuesch
▴ 10
0
votes
2
replies
1.2k
views
Diffbind: overlapping + Venn diagram
diffbind
9.5 years ago • updated 9.3 years ago
sergio.espeso-gil
• 0
0
votes
7
replies
1.7k
views
DiffBind fails to derive consensus peaksets
software error
chipseq
diffbind
updated 9.0 years ago by
Gord Brown
▴ 650 • written 9.0 years ago by
Nicolas Delhomme
▴ 320
50 results • Page
1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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