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interactionset
•
reset
1
vote
12
replies
2.9k
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How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
23 months ago
paria.alipour
• 0
1
vote
1
reply
2.3k
views
DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2
multifactorialdesign
interaction
InteractionSet
updated 7 months ago by
Michael Love
43k • written 7 months ago by
Integrative
• 0
1
vote
5
replies
2.0k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic
interactionset
9.5 years ago
Vivek.b
▴ 100
0
votes
2
replies
1.8k
views
Converting a GInteractions object to a dataframe
InteractionSet
4.5 years ago
noag
• 0
0
votes
2
replies
1.8k
views
Visualizing 4c-seq as arc
genomicinteractions
gviz
interactionset
updated 7.1 years ago by
liz.ingsimmons
▴ 140 • written 7.1 years ago by
ferbecneu
• 0
2
votes
1
reply
1.8k
views
Error to rename seqlevels in Granges interactions
interactionset
granges
updated 7.6 years ago by
Aaron Lun
★ 29k • written 7.6 years ago by
Vinicius Henrique da Silva
▴ 40
2
votes
1
reply
1.8k
views
Inflating interactionSets into a contact matrix
diffhic
hic
interactionset
contactmatrix
inflate
updated 8.2 years ago by
Aaron Lun
★ 29k • written 8.2 years ago by
hwick1
▴ 20
0
votes
1
reply
1.6k
views
Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4
Rcpp
InteractionSet
IRanges
Rle
updated 5.6 years ago by
Aaron Lun
★ 29k • written 5.6 years ago by
lklei001
• 0
0
votes
3
replies
1.5k
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet
GInteractions
2.0 years ago
Sarah
▴ 10
2
votes
1
reply
1.5k
views
cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet
structural variants
updated 9.5 years ago by
Aaron Lun
★ 29k • written 9.5 years ago by
tangming2005
▴ 200
0
votes
3
replies
1.4k
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
3.0 years ago
martin.grigorov
▴ 10
0
votes
1
reply
1.4k
views
How to load counts from existing count matrices in diffHic package
diffHic
HiC
InteractionSet
updated 5.7 years ago by
Aaron Lun
★ 29k • written 5.7 years ago by
girardot
• 0
1
vote
0
replies
947
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
2.5 years ago
Laureano Tomás-Daza
▴ 10
13 results • Page
1 of 1
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Comment: How to convert .raw data for use in xcms
by
TikTsossa33ssalpc
• 0
It sounds like your mzML conversion has a CV term that XCMS doesn t recognize, which often happens with newer vendor formats or outdated ms…
Comment: Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
by
TikTsossa33ssalpc
• 0
To calculate event numbers for boolean combinations in flow cytometry, you should use a logic gating tool or a script that processes popula…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa
by
Andrew Pattison
• 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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