Showing : interactionset • reset
1
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12
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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
0
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3
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656
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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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0
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416
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subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
10 months ago LaureTomas ▴ 10
0
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3
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775
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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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1.0k
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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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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
0
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1
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836
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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
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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
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
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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1.0k
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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
12 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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