Showing : interactionset • reset
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Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet GInteractions
3 months ago Sarah ▴ 10
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
7.8 years ago Vivek.b ▴ 100
2
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1
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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
2
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1
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1.3k
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Error to rename seqlevels in Granges interactions
interactionset granges
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 40
0
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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
0
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1
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832
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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
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1
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842
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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
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2
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1.0k
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Converting a GInteractions object to a dataframe
InteractionSet
2.8 years ago noag • 0
1
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12
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1.1k
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How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
10 weeks ago • updated 9 weeks ago paria.alipour • 0
2
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1
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1.0k
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cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet structural variants
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 190
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3
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771
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trying to generate an object from a virtual class ("DataFrame")
InteractionSet BuildReport
15 months ago martin.grigorov ▴ 10
1
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0
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413
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subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
10 months ago LaureTomas ▴ 10
12 results • Page 1 of 1
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Replies
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
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Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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