User: Vinicius Henrique da Silva

Reputation:
40
Status:
New User
Location:
Brazil
Last seen:
4 months, 2 weeks ago
Joined:
5 years, 1 month ago
Email:
v*****************@hotmail.com

Posts by Vinicius Henrique da Silva

<prev • 44 results • page 1 of 5 • next >
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openPrimeR can't find external dependencies
... I am trying to install the package `openPrimeRui`. This package requires some external dependencies (not R packages), which are checked once you open the Shiny app: library(openPrimeRui) if (interactive()) { startApp() } [![enter image description here][1]][1] [1]: https:// ...
openprimerui openprimer written 4 months ago by Vinicius Henrique da Silva40
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Make UpSet function display numbers above the bars
... I am using the `ComplexHeatmap` package to represent the intersection among different `GRanges`. The vignette has some nice example to plot it: library(circlize) library(ComplexHeatmap) library(GenomicRanges) lt2 = lapply(1:4, function(i) generateRandomBed()) lt2 = lapply(lt2, f ...
complexheatmap written 7 months ago by Vinicius Henrique da Silva40 • updated 7 months ago by Zuguang Gu170
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Create a matrix to show overlaps among multiple GRanges
... I am trying to find a way to efficiently extract a matrix showing '0' or '1' when comparing different `GRange` objects. In my example: gr.1 <- regioneR::createRandomRegions(nregions=1000, length.mean=500000, length.sd=30000) gr.2 <- regioneR::createRandomRegions(nregions=1000, length. ...
genomicranges granges R written 7 months ago by Vinicius Henrique da Silva40 • updated 7 months ago by James W. MacDonald51k
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Go back to GRanges used as RaggedExperiment input
... I am trying to get back to the input objects of a RaggedExperiment object. Using the example in the manual: sample1 <- GRanges( c(A = "chr1:1-10:-", B = "chr1:8-14:+", C = "chr2:15-18:+"), score = 3:5) sample2 <- GRanges( c(D = "chr1:1-10:-", E = "chr2:11-18:+" ...
raggedexperiment written 9 months ago by Vinicius Henrique da Silva40 • updated 9 months ago by Marcel Ramos ♦♦ 410
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Error to rename seqlevels in Granges interactions
... I am trying to rename the seqlevels in an interactionSet object. The syntax for common GRanges don't work in an interaction set. Any ideas how to make it work then?   library(GenomicRanges) gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10)) index.epistasis <- expand.grid( ...
granges interactionset written 15 months ago by Vinicius Henrique da Silva40 • updated 15 months ago by Aaron Lun25k
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Write gds in parallel
... I am trying to write values at a certain GDS node in parallel. I was not able to figure out what I am doing wrong. I have tried the following: ​# Load data data(hapmap_geno) # Create a gds file snpgdsCreateGeno("test.gds", genmat = hapmap_geno$genotype, sample.id = hapmap_geno$sample.id, snp ...
biocparallel snprelate gds written 18 months ago by Vinicius Henrique da Silva40 • updated 17 months ago by zhengx30
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Comment: C: Transform index to chromosome in DECIPHER package
... Hi Erik, thank you for your prompt answer. In your example you used 'XStringSet; instead 'FASTA' directly. Running the analysis again using your example will work fine. However, would be nice to understand what I have already, where I used the 'FASTA' files. As far I understand, the 'Seqs2DB' functi ...
written 21 months ago by Vinicius Henrique da Silva40
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Transform index to chromosome in DECIPHER package
... I am trying to understand how the index from the synteny analysis in the DECIPHER package can be translated into chromosomes. I basically used what is in the official website: # load the DECIPHER library in R library(DECIPHER) # specify the path to each FASTA file (in quotes) # each genome must b ...
decipher written 21 months ago by Vinicius Henrique da Silva40 • updated 21 months ago by Erik Wright140
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Avoid 'dStr8' format in the GDS files
... I would like to use a GDS file to an external software called SNPhylo. However, I am getting an error when trying to use this external software:   Error in index.gdsn(gdsobj, "sample.id") : No class name 'dStr8' in the GDS system. Reading the news about the GDS files in GitHub, this 'dStr8' forma ...
snprelatesnp written 2.8 years ago by Vinicius Henrique da Silva40
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Conflicting results in 'overlapPermTest' function from regioneR package
... I am aware that non-reproducible questions are annoying. However, I am not sure how to reproduce my problem without my original data (and consequently to large to be included here).  I have two groups of genomic ranges, 'Nre' and 'Re', and I compared separately how random are their overlap with CpG ...
regioner written 2.8 years ago by Vinicius Henrique da Silva40 • updated 2.8 years ago by bernatgel120

Latest awards to Vinicius Henrique da Silva

Popular Question 9 months ago, created a question with more than 1,000 views. For Error: package ‘snpMatrix’ is not available (for R version 3.2.2)
Popular Question 9 months ago, created a question with more than 1,000 views. For Error: package ‘snpMatrix’ is not available (for R version 3.2.2)
Popular Question 17 months ago, created a question with more than 1,000 views. For Error: package ‘snpMatrix’ is not available (for R version 3.2.2)
Supporter 3.5 years ago, voted at least 25 times.

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