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InteractionSet
•
reset
1
vote
12
replies
962
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
5 weeks ago • updated 4 weeks ago
paria.alipour
• 0
1
vote
5
replies
1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic
interactionset
7.7 years ago
Vivek.b
▴ 100
0
votes
3
replies
594
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet
GInteractions
10 weeks ago
Sarah
▴ 10
0
votes
3
replies
722
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
14 months ago
martin.grigorov
▴ 10
0
votes
2
replies
1.2k
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
0
votes
2
replies
955
views
Converting a GInteractions object to a dataframe
InteractionSet
2.7 years ago
noag
• 0
0
votes
1
reply
798
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
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
2
votes
1
reply
1.3k
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
0
votes
1
reply
795
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
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
0
replies
365
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
8 months ago
LaureTomas
▴ 10
12 results • Page
1 of 1
Recent ...
Replies
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
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
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