User: rulicosentino

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Posts by rulicosentino

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DiffHic package - heatmap generation from normalized data
... Hi,  I would like to know how to generate an interaction heatmap, like the one is generated with plotPlaid, after normalizing the input data. More precisely, I would like to generate a heatmap after iterative correction of interaction intensities (correctedContact). Thanks,     ...
diffhic written 4.0 years ago by rulicosentino0 • updated 4.0 years ago by Aaron Lun25k
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diffHic package plotPlaid. Visualize multiple inter-chromosomal and intra-chromosomal interactions in the same heatmap
... Hi,  Is it possible to draw a heatmap with plotPlaid from some (or all) chromosomes together? How?   ...
granges diffhic written 4.0 years ago by rulicosentino0 • updated 4.0 years ago by Aaron Lun25k
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DiffHic-package. Identify the name of bins with over or underrepresentation of reads mapped -marginCounts- . Extracting data from DIList objects
... Hi, I am following the diffHic tutorial using my datasets, consisting in two biological replicates for one condition and four biological replicates for another condition. I have three questions which I am writing below: 1st question: I am in the step 3.4 of the tutorial ("Counting into single bin ...
diffhic margincounts squarecounts dilist written 4.4 years ago by rulicosentino0 • updated 4.4 years ago by Aaron Lun25k
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Answer: A: diffHic-package_PreparePairs-function-error:"missing chromosomes in cut site lis
... Hi Aaron, thank you for your answer! I ran what you told me, and the names of the chromosomes were different. The original names in the fasta file were something like :  > chr1 | organism=Homo sapiens | version=2015 | length= 3000000 > chr2 | organism=Homo sapiens | version=2015 | length= ...
written 4.5 years ago by rulicosentino0
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diffHic-package_PreparePairs-function-error:"missing chromosomes in cut site list"
... Hi, I am trying to learn (and apply) the tools of the package "diffHic" (Differential analysisi of Hi-C data) to analyze  Hi-C datasets and compare them. I am following the user's guide. I am working with a genome that is not available as Biostrings object.   To obtain a restriction-fragmented gen ...
diffhic preparepairs hi-c cutgenome written 4.5 years ago by rulicosentino0

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Popular Question 4.0 years ago, created a question with more than 1,000 views. For diffHic-package_PreparePairs-function-error:"missing chromosomes in cut site list"

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