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InteractionSet
•
reset
1
vote
12
replies
1.0k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
9 weeks ago • updated 8 weeks ago
paria.alipour
• 0
0
votes
3
replies
644
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet
GInteractions
3 months ago
Sarah
▴ 10
1
vote
0
replies
395
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
9 months ago
LaureTomas
▴ 10
0
votes
3
replies
754
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
15 months ago
martin.grigorov
▴ 10
0
votes
2
replies
990
views
Converting a GInteractions object to a dataframe
InteractionSet
2.8 years ago
noag
• 0
0
votes
1
reply
830
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4
Rcpp
InteractionSet
IRanges
Rle
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
lklei001
• 0
0
votes
1
reply
822
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
girardot
• 0
0
votes
2
replies
1.2k
views
Visualizing 4c-seq as arc
genomicinteractions
gviz
interactionset
updated 5.4 years ago by
liz.ingsimmons
▴ 140 • written 5.4 years ago by
ferbecneu
• 0
2
votes
1
reply
1.3k
views
Error to rename seqlevels in Granges interactions
interactionset
granges
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 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 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
hwick1
▴ 20
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
1.0k
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
12 results • Page
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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