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dba.count
•
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0
votes
0
replies
123
views
DiffBind3: all samples have 0 counts for all genes. check the counting script
dba.count
DiffBind3
3 months ago
yang
• 0
1
vote
6
replies
442
views
DiffBind dba.count Error in if (sum(tokeep) < length(tokeep))
DiffBind
dba.count
updated 3 months ago by
Rory Stark
★ 4.4k • written 4 months ago by
tjhwangxiong
• 0
1
vote
3
replies
395
views
issue with DiffBind dba.count
bam
bai
DiffBind
dba.count
Diffbind
updated 9 months ago by
Rory Stark
★ 4.4k • written 9 months ago by
mtsompana
▴ 10
0
votes
6
replies
1.5k
views
DiffBind: Error in heights * sapply(called, function(x) x)
diffbind
dba.count
summits
updated 16 months ago by
Rory Stark
★ 4.4k • written 4.5 years ago by
zhaolin20042008
• 0
0
votes
1
reply
254
views
diffbind counts as same values
diffbind
dba.count
dba.report
updated 2.6 years ago by
Rory Stark
★ 4.4k • written 2.7 years ago by
chadnewton
• 0
0
votes
4
replies
814
views
How to produce the fraction of reads in peaks (FRiP) using DiffBind
DiffBind
FRiP
ATAC-Seq
dba.show
dba.count
updated 3.2 years ago by
Rory Stark
★ 4.4k • written 3.2 years ago by
Gary
▴ 20
0
votes
1
reply
642
views
Handing duplicates in DiffBind
diffbind
dba.count
bRemoveDuplicates
bUseSummarizeOverlaps
updated 3.2 years ago by
Rory Stark
★ 4.4k • written 3.2 years ago by
loretta
• 0
1
vote
1
reply
765
views
how to retrieve binding affinity matrix in diffbind
diffbind
dba.count
updated 3.2 years ago by
Rory Stark
★ 4.4k • written 3.2 years ago by
hamaor
• 0
0
votes
1
reply
467
views
dba.count generates less ranges than input peakset
diffbind
dba.count
dba.peakset
updated 4.1 years ago by
Rory Stark
★ 4.4k • written 4.2 years ago by
pau.rodriguez.sodupe
• 0
3
votes
7
replies
1.2k
views
dba.count with pre-defined regions
dba.count
dba
chipseq
diffbind
updated 4.4 years ago by
Rory Stark
★ 4.4k • written 4.5 years ago by
sylvia
▴ 10
0
votes
6
replies
1.2k
views
Warnings when update DiffBind and running errors
diffbind
atac-seq
dba.count
updated 4.5 years ago by
Rory Stark
★ 4.4k • written 4.5 years ago by
zhaolin20042008
• 0
3
votes
9
replies
1.4k
views
Error When using dba.count() in DiffBind
dba.count
atac-seq
diffbind
updated 4.5 years ago by
Gord Brown
▴ 640 • written 4.5 years ago by
ew152
• 0
0
votes
1
reply
537
views
Error with dba.count function code
diffbind
dba.count
atac-seq
updated 4.6 years ago by
Gord Brown
▴ 640 • written 4.6 years ago by
VCLRAC001
• 0
0
votes
3
replies
865
views
Error with dba.count function
diffbind
dba.count
updated 4.6 years ago by
Gord Brown
▴ 640 • written 4.6 years ago by
VCLRAC001
• 0
1
vote
5
replies
1.4k
views
Problem reading Bed file using dba.count in DiffBind
DiffBind
dba.count
Chip-Seq
Differential analysis
updated 14 months ago by
Goku
• 0 • written 4.7 years ago by
urjaswita
▴ 40
0
votes
2
replies
649
views
Diffbind results - non uniform width
diffbind
dba.count
updated 5.0 years ago by
Rory Stark
★ 4.4k • written 5.0 years ago by
YaGalbi
▴ 20
0
votes
1
reply
1.3k
views
DiffBind - Difference in counting methodology when summits option in dba.count is on?
diffbind
dba.count
summits
updated 5.3 years ago by
Rory Stark
★ 4.4k • written 5.5 years ago by
julien.bryois
• 0
1
vote
2
replies
720
views
The descriptions of score methods in DiffBind
DiffBind
dba.count
score
manual
PDF
updated 5.4 years ago by
Rory Stark
★ 4.4k • written 5.4 years ago by
Gary
▴ 20
0
votes
3
replies
828
views
DiffBind dba.count() seqfault
diffbind
dba.count
6.0 years ago
em540
• 0
1
vote
3
replies
1.5k
views
[DiffBind] Memory issues with dba.count()
diffbind
bigmemory
matrix
dba.count
updated 6.8 years ago by
Rory Stark
★ 4.4k • written 6.8 years ago by
enricoferrero
▴ 610
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Comment: CPM after RUVseq
by
James W. MacDonald
59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq
by
James W. MacDonald
59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq
by
Jess
• 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error
by
Laurent Gatto
1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue
by
shepherl
3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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