Showing : InteractionSet • reset
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How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
14 months ago paria.alipour • 0
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3
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1.1k
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Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet GInteractions
15 months ago Sarah ▴ 10
1
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0
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748
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subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
21 months ago LaureTomas ▴ 10
0
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3
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1.2k
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trying to generate an object from a virtual class ("DataFrame")
InteractionSet BuildReport
2.2 years ago martin.grigorov ▴ 10
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2
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1.5k
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Converting a GInteractions object to a dataframe
InteractionSet
3.8 years ago noag • 0
0
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1
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1.3k
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Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
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1
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1.2k
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How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
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2
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1.6k
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Visualizing 4c-seq as arc
genomicinteractions gviz interactionset
updated 6.4 years ago by ▴ 140 • written 6.4 years ago by • 0
2
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1
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1.6k
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Error to rename seqlevels in Granges interactions
interactionset granges
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 40
2
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1
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1.5k
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Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
1
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5
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1.7k
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diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
8.7 years ago Vivek.b ▴ 100
2
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1
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1.3k
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cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet structural variants
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 200
12 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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