Showing : interactionset • reset
1
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5
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1.3k
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diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
7.7 years ago Vivek.b ▴ 100
2
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1
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1.3k
views
Error to rename seqlevels in Granges interactions
interactionset granges
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 40
2
votes
1
reply
1.2k
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Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 20
0
votes
2
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1.2k
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Visualizing 4c-seq as arc
genomicinteractions gviz interactionset
updated 5.4 years ago by ▴ 140 • written 5.4 years ago by • 0
2
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1
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1.0k
views
cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet structural variants
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 190
1
vote
12
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1.0k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
8 weeks ago paria.alipour • 0
0
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2
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987
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 ★ 28k • written 3.9 years ago by • 0
0
votes
1
reply
821
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How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
0
votes
3
replies
751
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet BuildReport
15 months ago martin.grigorov ▴ 10
0
votes
3
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641
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Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet GInteractions
3 months ago Sarah ▴ 10
1
vote
0
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395
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subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
9 months ago LaureTomas ▴ 10
12 results • Page 1 of 1
Recent ...
Replies
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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