Showing : InteractionSet • reset
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DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in a Four-Factor Design
DESeq2 multifactorialdesign interaction InteractionSet
updated 5 months ago by 43k • written 5 months ago by • 0
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12
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2.7k
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How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
21 months ago paria.alipour • 0
0
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3
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1.4k
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Cannot use findOverlaps with 2 GInteractions objects with different ranges.
InteractionSet GInteractions
22 months ago Sarah ▴ 10
1
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0
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899
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subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
2.4 years ago Laureano Tomás-Daza ▴ 10
0
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3
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1.3k
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trying to generate an object from a virtual class ("DataFrame")
InteractionSet BuildReport
2.8 years ago martin.grigorov ▴ 10
0
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2
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1.8k
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Converting a GInteractions object to a dataframe
InteractionSet
4.4 years ago noag • 0
0
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1
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1.5k
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Resources to learn about s4 object extension/inheritance, custom print methods, and new operations
S4 Rcpp InteractionSet IRanges Rle
updated 5.4 years ago by ★ 29k • written 5.4 years ago by • 0
0
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1
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1.3k
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How to load counts from existing count matrices in diffHic package
diffHic HiC InteractionSet
updated 5.6 years ago by ★ 29k • written 5.6 years ago by • 0
0
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2
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1.8k
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Visualizing 4c-seq as arc
genomicinteractions gviz interactionset
updated 7.0 years ago by ▴ 140 • written 7.0 years ago by • 0
2
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1
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1.7k
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Error to rename seqlevels in Granges interactions
interactionset granges
updated 7.4 years ago by ★ 29k • written 7.4 years ago by ▴ 40
2
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1
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1.7k
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Inflating interactionSets into a contact matrix
diffhic hic interactionset contactmatrix inflate
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 20
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5
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1.9k
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diffHiC differential HiC analysis starting from Ginteractions object
diffhic interactionset
9.3 years ago Vivek.b ▴ 100
2
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1
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1.4k
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cluster (only one end overlapping) breakpoints using InteractionSet
InteractionSet structural variants
updated 9.3 years ago by ★ 29k • written 9.3 years ago by ▴ 200
13 results • Page 1 of 1
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Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
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Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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