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interactionset
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1
vote
12
replies
1.8k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
11 months ago
paria.alipour
• 0
0
votes
3
replies
1.1k
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet
GInteractions
13 months ago
Sarah
▴ 10
1
vote
0
replies
700
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
19 months ago
LaureTomas
▴ 10
0
votes
3
replies
1.1k
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
2.1 years ago
martin.grigorov
▴ 10
0
votes
2
replies
1.4k
views
Converting a GInteractions object to a dataframe
InteractionSet
3.6 years ago
noag
• 0
0
votes
1
reply
1.2k
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4
Rcpp
InteractionSet
IRanges
Rle
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
lklei001
• 0
0
votes
1
reply
1.1k
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
girardot
• 0
0
votes
2
replies
1.5k
views
Visualizing 4c-seq as arc
genomicinteractions
gviz
interactionset
updated 6.2 years ago by
liz.ingsimmons
▴ 140 • written 6.2 years ago by
ferbecneu
• 0
2
votes
1
reply
1.5k
views
Error to rename seqlevels in Granges interactions
interactionset
granges
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
Vinicius Henrique da Silva
▴ 40
2
votes
1
reply
1.5k
views
Inflating interactionSets into a contact matrix
diffhic
hic
interactionset
contactmatrix
inflate
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
hwick1
▴ 20
1
vote
5
replies
1.6k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic
interactionset
8.5 years ago
Vivek.b
▴ 100
2
votes
1
reply
1.2k
views
cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet
structural variants
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 years ago by
tangming2005
▴ 200
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Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.7k
biostars.org and the [bioinformatics reddit][1] are suitable and have much larger audience than this forum here. [1]: https://www.reddi…
Comment: Overcoming confounding in batch effect correction
by
bbao
▴ 10
Thank you! And apologies for posting here. Do you know which forum I should go to in the future for questions like these?
Comment: For some reason I can't update BiocManager to 3.20
by
shepherl
4.1k
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this…
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.7k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Comment: MEDIPS - error using MEDIPS.CpGenrich
by
sg
• 0
I have the same error when I use 22 chrs with the paramenters chr.select: Error in h(simpleError(msg, call)) : error in evaluating the …
Votes
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
Comment: Overcoming confounding in batch effect correction
Overcoming confounding in batch effect correction
Answer: Standardization of rlog transformed counts before PCA
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