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DiffBind
•
reset
1
vote
25
replies
3.3k
views
DiffBind spike-in normalization
DiffBind
18 months ago
yuhuihui2011
• 0
8
votes
20
replies
4.5k
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
updated 2.2 years ago by
Rory Stark
★ 5.1k • written 3.3 years ago by
Sam
▴ 10
5
votes
19
replies
5.8k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 8 months ago by
liz.lamarca
• 0 • written 2.7 years ago by
kwangbom
▴ 10
5
votes
17
replies
1.8k
views
DiffBind : More fragment sizes than libraries
diffbind
updated 6.9 years ago by
Rory Stark
★ 5.1k • written 6.9 years ago by
ZheFrench
▴ 40
1
vote
16
replies
3.6k
views
Error: could not find function "dba"
software error
diffbind
dba
7.5 years ago • updated 7.4 years ago
mmarins
• 0
3
votes
16
replies
4.3k
views
DiffBind differential binding normalization with different levels of binding
diffbind
updated 8.6 years ago by
Rory Stark
★ 5.1k • written 8.6 years ago by
igor
▴ 40
1
vote
16
replies
4.8k
views
DiffBind Batch Effect
diffbind
atac
6.9 years ago
niu.shengyong
• 0
5
votes
16
replies
4.5k
views
Exporting dba.count result as a data frame
diffbind
9.0 years ago
mm2489
▴ 10
0
votes
14
replies
2.4k
views
got 0 significant differential bound (DB)
diffbind
6.9 years ago
mforoo1
• 0
0
votes
14
replies
2.2k
views
Path to file in windows
bioconductor
R
windows
diffbind
updated 7.0 years ago by
Gord Brown
▴ 650 • written 7.0 years ago by
jorrenkuster
• 0
1
vote
14
replies
1.9k
views
error: DBA object is already formed from a consensus peakset
DiffBind
3.2 years ago
ahua217
▴ 10
7
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by
Rory Stark
★ 5.1k • written 10 months ago by
Chris
• 0
0
votes
13
replies
1.5k
views
Does DiffBind make consensus peaks sets for samples from a given condition (e.g. case control)?
dba.analyze
DiffBind
@rory-stark-5741
13 months ago
tahir.msajid
• 0
8
votes
13
replies
2.7k
views
Help with Error in DiffBind
DiffBind
ATACSeq
13 months ago • updated 12 months ago
Chris
• 0
2
votes
12
replies
2.0k
views
Too much data for Diffbind
DiffBind
18 months ago • updated 17 months ago
littlefishes20
▴ 10
3
votes
12
replies
3.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind
ChIPseq
updated 2.7 years ago by
Rory Stark
★ 5.1k • written 4.6 years ago by
zhenfeng.liu1
▴ 20
3
votes
11
replies
3.2k
views
How to get all possible comparisons in DiffBind
diffbind
updated 2.2 years ago by
Rory Stark
★ 5.1k • written 5.3 years ago by
bony.dekumar
• 0
5
votes
10
replies
1.8k
views
Learning DiffBind - some basic questions
DiffBind
updated 3.1 years ago by
Rory Stark
★ 5.1k • written 3.3 years ago by
Sam
▴ 10
1
vote
10
replies
2.3k
views
DiffBind for ATACseq without replicates
DiffBind
ATACseq
replicate
updated 3.4 years ago by
Rory Stark
★ 5.1k • written 3.5 years ago by
CodeAway
▴ 70
1
vote
10
replies
1.5k
views
DiffBind: Values of Called1 and Called2 do not appear to coincide with input peaks
DiffBind
updated 2.2 years ago by
Rory Stark
★ 5.1k • written 2.3 years ago by
Ian
• 0
2
votes
10
replies
2.0k
views
DiffBind consensus peak help
diffbind
r
chipseq
updated 6.6 years ago by
Rory Stark
★ 5.1k • written 6.6 years ago by
reubenmcgregor88
• 0
0
votes
10
replies
1.7k
views
Error report when using dab() in Diffbind
DiffBind
3.4 years ago
ahua217
▴ 10
3
votes
9
replies
2.6k
views
Error When using dba.count() in DiffBind
dba.count
atac-seq
diffbind
updated 6.4 years ago by
Gord Brown
▴ 650 • written 6.4 years ago by
ew152
• 0
1
vote
9
replies
1.8k
views
DiffBind is losing peaks
DiffBind
3.5 years ago • updated 3.4 years ago
Sebastian
• 0
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
3
votes
9
replies
3.5k
views
DiffBind BED output with score
diffbind
differential binding analysis
updated 7.2 years ago by
Rory Stark
★ 5.1k • written 7.2 years ago by
rbronste
▴ 60
16
votes
9
replies
6.5k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 6.5 years ago by
Rory Stark
★ 5.1k • written 8.1 years ago by
florian.noack
▴ 60
3
votes
9
replies
2.1k
views
retreiving peak caller fold enrichments after generating consensus peakset in DiffBind
diffbind
updated 9.0 years ago by
Rory Stark
★ 5.1k • written 9.0 years ago by
mm2489
▴ 10
5
votes
9
replies
1.9k
views
DESeq2 baseMean from DiffBind summarizedExperiment
deseq2
diffbind
basemean
summarizedexperiment
5.7 years ago
rbronste
▴ 60
2
votes
8
replies
2.0k
views
DiffBind -- Error: No sites have activity greater than minMaxval
DiffBind
updated 19 months ago by
wxd_qf
• 0 • written 2.9 years ago by
Alexandre
• 0
2
votes
8
replies
1.3k
views
Difbind: output rows from binding heatmap plot
diffbind
updated 7.6 years ago by
Rory Stark
★ 5.1k • written 7.6 years ago by
svohra
• 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
0
votes
8
replies
1.4k
views
Regarding general understanding of DiffBind
diffbind
heatmap
7.8 years ago
shubhibartaria
▴ 10
4
votes
8
replies
2.2k
views
ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single sample
DiffBind
ChIPQC
8.2 years ago
JD
▴ 10
1
vote
8
replies
1.9k
views
Extracting raw read counts in DiffBind consensus peak set
DiffBind
updated 3.9 years ago by
Rory Stark
★ 5.1k • written 3.9 years ago by
hasse.bossenbroek
• 0
0
votes
8
replies
1.1k
views
Question about Diffbind counts
DiffBind
15 months ago
slrpatty
• 0
5
votes
8
replies
2.1k
views
how to construct a DBA object from count matrix
ChIPSeq
ATACSeq
differentially_occupied
DiffBind
updated 22 months ago by
Johanna Hardin
▴ 20 • written 2.8 years ago by
pegah.taklifi
▴ 30
0
votes
8
replies
1.1k
views
Question on bgzf_read error
diffbind
4.4 years ago
Kath
• 0
0
votes
8
replies
1.9k
views
DiffBind and paired end data
DiffBind
DiffBind
10.1 years ago
Rory Stark
★ 5.1k
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
6
votes
8
replies
2.4k
views
Interaction with DESeq2 via DiffBind
diffbind
deseq2
interactions
updated 3.3 years ago by
pierre.marin
• 0 • written 6.5 years ago by
rbronste
▴ 60
1
vote
8
replies
2.3k
views
DiffBind 'mc.cores' > 1 is not supported on Windows
DiffBind
3.3 years ago
GM
▴ 10
3
votes
8
replies
2.3k
views
How DiffBind run PCA based on peak data?
DiffBind
updated 3.5 years ago by
Rory Stark
★ 5.1k • written 6.6 years ago by
Gary
▴ 20
1
vote
8
replies
1.3k
views
Diffbind multiple blocking factor
diffbind
rory stark
chip seq
updated 3.5 years ago by
Rory Stark
★ 5.1k • written 4.0 years ago by
bioinfouser2
▴ 10
1
vote
8
replies
1.2k
views
The compare result is different in score and Conc in DiffBind
DiffBind
3.2 years ago
Guandong Shang
▴ 40
0
votes
7
replies
1.9k
views
DiffBind:Treatments + second factor
DiffBind
diffbind
updated 9.4 years ago by
Rory Stark
★ 5.1k • written 9.5 years ago by
sergio.espeso-gil
• 0
4
votes
7
replies
2.5k
views
Normalization in DiffBind for Atac-seq
DiffBind
3.4 years ago
Debayan
▴ 20
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
0
votes
7
replies
1.8k
views
Error report when loading a 0-byte bed file for DBA object in Diffbind
DiffBind
3.4 years ago • updated 3.2 years ago
ahua217
▴ 10
3
votes
7
replies
2.0k
views
dba.count with pre-defined regions
dba.count
dba
chipseq
diffbind
updated 6.4 years ago by
Rory Stark
★ 5.1k • written 6.4 years ago by
sylvia
▴ 10
50 results • Page
1 of 1
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Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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