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
9 weeks ago • updated 8 weeks ago paria.alipour • 0
0
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3
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644
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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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395
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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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754
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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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989
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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
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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
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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
views
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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1.0k
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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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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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