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
14 months ago paria.alipour • 0
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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752
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subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
22 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
2.3 years ago martin.grigorov ▴ 10
0
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2
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1.5k
views
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
views
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
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
0
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2
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1.6k
views
Visualizing 4c-seq as arc
genomicinteractions gviz interactionset
updated 6.4 years ago by ▴ 140 • written 6.4 years ago by • 0
2
votes
1
reply
1.6k
views
Error to rename seqlevels in Granges interactions
interactionset granges
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 40
2
votes
1
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1.5k
views
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
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
8.7 years ago Vivek.b ▴ 100
2
votes
1
reply
1.3k
views
cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet structural variants
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 200
12 results • Page 1 of 1
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Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness by ATpoint ★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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