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InteractionSet
•
reset
1
vote
5
replies
1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic
interactionset
7.7 years ago
Vivek.b
▴ 100
2
votes
1
reply
1.2k
views
Error to rename seqlevels in Granges interactions
interactionset
granges
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Vinicius Henrique da Silva
▴ 40
2
votes
1
reply
1.2k
views
Inflating interactionSets into a contact matrix
diffhic
hic
interactionset
contactmatrix
inflate
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
hwick1
▴ 20
0
votes
2
replies
1.1k
views
Visualizing 4c-seq as arc
genomicinteractions
gviz
interactionset
updated 5.3 years ago by
liz.ingsimmons
▴ 140 • written 5.3 years ago by
ferbecneu
• 0
2
votes
1
reply
1.0k
views
cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet
structural variants
updated 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
tangming2005
▴ 190
1
vote
12
replies
957
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
5 weeks ago • updated 29 days ago
paria.alipour
• 0
0
votes
2
replies
953
views
Converting a GInteractions object to a dataframe
InteractionSet
2.7 years ago
noag
• 0
0
votes
1
reply
796
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4
Rcpp
InteractionSet
IRanges
Rle
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
lklei001
• 0
0
votes
1
reply
792
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
girardot
• 0
0
votes
3
replies
718
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
14 months ago
martin.grigorov
▴ 10
0
votes
3
replies
593
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet
GInteractions
10 weeks ago
Sarah
▴ 10
1
vote
0
replies
363
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
8 months ago
LaureTomas
▴ 10
12 results • Page
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Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
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