Showing : InteractionSet • reset
1
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12
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1.0k
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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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3
replies
643
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet GInteractions
3 months ago Sarah ▴ 10
1
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0
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395
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
9 months ago LaureTomas ▴ 10
0
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3
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752
views
trying to generate an object from a virtual class ("DataFrame")
InteractionSet BuildReport
15 months ago martin.grigorov ▴ 10
0
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2
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987
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Converting a GInteractions object to a dataframe
InteractionSet
2.8 years ago noag • 0
0
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1
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830
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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
0
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1
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822
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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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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
votes
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
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1
reply
1.2k
views
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
1
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5
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1.3k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
7.7 years ago Vivek.b ▴ 100
2
votes
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
12 results • Page 1 of 1
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Comment: Different Shrunk Log2FC according with reference by Michael Love 41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Votes
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
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