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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
4.6k
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
updated 2.3 years ago by
Rory Stark
★ 5.2k • written 3.3 years ago by
Sam
▴ 10
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 8 months ago by
liz.lamarca
• 0 • written 2.8 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
★ 5.2k • 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
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
★ 5.2k • 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
2.0k
views
error: DBA object is already formed from a consensus peakset
DiffBind
3.2 years ago
ahua217
▴ 10
8
votes
13
replies
1.8k
views
Interpret plot from DiffBind
DiffBind
updated 10 months ago by
Rory Stark
★ 5.2k • written 11 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
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
★ 5.2k • written 4.6 years ago by
zhenfeng.liu1
▴ 20
4
votes
11
replies
3.3k
views
How to get all possible comparisons in DiffBind
diffbind
updated 2.2 years ago by
Rory Stark
★ 5.2k • written 5.3 years ago by
bony.dekumar
▴ 10
5
votes
10
replies
1.8k
views
Learning DiffBind - some basic questions
DiffBind
updated 3.1 years ago by
Rory Stark
★ 5.2k • written 3.3 years ago by
Sam
▴ 10
1
vote
10
replies
2.3k
views
DiffBind for ATACseq without replicates
DiffBind
ATACseq
replicate
updated 3.5 years ago by
Rory Stark
★ 5.2k • 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 2.3 years ago by
Rory Stark
★ 5.2k • 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
★ 5.2k • written 6.6 years ago by
reubenmcgregor88
• 0
0
votes
10
replies
1.7k
views
Error report when using dab() in Diffbind
DiffBind
3.5 years ago • updated 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 6.5 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
★ 5.2k • 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
★ 5.2k • 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
★ 5.2k • 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
★ 5.2k • written 7.7 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
2.0k
views
Extracting raw read counts in DiffBind consensus peak set
DiffBind
updated 3.9 years ago by
Rory Stark
★ 5.2k • 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
2.2k
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
4.5 years ago
Kath
• 0
0
votes
8
replies
1.9k
views
DiffBind and paired end data
DiffBind
DiffBind
10.2 years ago • updated 10.1 years ago
Rory Stark
★ 5.2k
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
★ 5.2k • 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
★ 5.2k • 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
3.3 years ago • updated 3.2 years ago
Guandong Shang
▴ 40
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
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
★ 5.2k • written 6.4 years ago by
sylvia
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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