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Showing :
InteractionSet
•
reset
1
vote
12
replies
915
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
26 days ago • updated 20 days ago
paria.alipour
• 0
0
votes
3
replies
573
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet
GInteractions
9 weeks ago • updated 8 weeks ago
Sarah
▴ 10
0
votes
0
replies
349
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet
subsetByOverlaps
GenomicInteractions
8 months ago
LaureTomas
• 0
0
votes
3
replies
708
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet
BuildReport
13 months ago
martin.grigorov
▴ 10
0
votes
2
replies
947
views
Converting a GInteractions object to a dataframe
InteractionSet
2.7 years ago
noag
• 0
0
votes
1
reply
790
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
786
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
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
1.2k
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
1
vote
5
replies
1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic
interactionset
7.6 years ago
Vivek.b
▴ 100
2
votes
1
reply
1.0k
views
cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet
structural variants
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
tangming2005
▴ 190
12 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
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Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
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