Showing : InteractionSet • reset
1
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12
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1.7k
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How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
10 months ago paria.alipour • 0
0
votes
3
replies
986
views
Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet GInteractions
11 months ago Sarah ▴ 10
1
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0
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665
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
17 months ago LaureTomas ▴ 10
0
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3
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1.1k
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trying to generate an object from a virtual class ("DataFrame")
InteractionSet BuildReport
23 months ago martin.grigorov ▴ 10
0
votes
2
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1.4k
views
Converting a GInteractions object to a dataframe
InteractionSet
3.5 years ago • updated 3.4 years ago noag • 0
0
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1
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1.1k
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Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
0
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1
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1.1k
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How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
votes
2
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1.5k
views
Visualizing 4c-seq as arc
genomicinteractions gviz interactionset
updated 6.0 years ago by ▴ 140 • written 6.0 years ago by • 0
2
votes
1
reply
1.5k
views
Error to rename seqlevels in Granges interactions
interactionset granges
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 40
2
votes
1
reply
1.4k
views
Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 20
1
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5
replies
1.6k
views
diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
8.4 years ago Vivek.b ▴ 100
2
votes
1
reply
1.2k
views
cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet structural variants
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 200
12 results • Page 1 of 1
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Replies
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Comment: Packages don't update, but no error or warning is thrown by neighsanlo • 0
This is useful information.
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by freemanmclaughlin9969289 • 0
Tools such as Pathway Analysis with Deweighting of Overlapping Genes ([block blast][1]) or Gene Set Enrichment Analysis for Single Cell RNA…
Comment: How to get around the warning message: mzR has been built against a different Rc by Nan • 0
Hello, I was wondering if you were able to resolve this issue? I've recently encountered a similar problem and would like to ask for your a…
Votes
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
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