User: Vinicius Henrique da Silva

Reputation:
20
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New User
Location:
Brazil
Last seen:
1 month ago
Joined:
3 years, 6 months ago
Email:
v*****************@hotmail.com

Posts by Vinicius Henrique da Silva

<prev • 38 results • page 1 of 4 • next >
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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 5 weeks ago by Vinicius Henrique da Silva20
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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 6 weeks ago by Vinicius Henrique da Silva20 • updated 6 weeks ago by Erik Wright100
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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 13 months ago by Vinicius Henrique da Silva20
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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 13 months ago by Vinicius Henrique da Silva20 • updated 13 months ago by bernatgel70
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Identify in tandem repeats with Bioconductor
... I would like to identify the regions with repeated patterns in a given genome. Let's say that I need to identify [TA]n regions, were 'n' is a variable number of repeats. I thought in a loop to resolve the problem, however, it will take a long time and will produce redundant regions. Thus, I would l ...
biostrings written 17 months ago by Vinicius Henrique da Silva20 • updated 17 months ago by Hervé Pagès ♦♦ 13k
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Fill the color in a graph in a reverse scale - gtrellis
...    I would like to fill the graph within the polygons instead out of it.  library(gtrellis) library(circlize) tiff("plot.tiff", units="in", width=11, height=8.5, res=300, compress = "lzw") load(system.file("extdata", "DMR.RData", package = "circlize")) DMR_hyper_density = ci ...
gtrellis written 19 months ago by Vinicius Henrique da Silva20
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Plot just one y label in gtrellis
... I would like to plot just one y-axis label for each different track instead one for each chromosome in gtrellis package (In the manual example exemplified below the title "density" is repeated several times). I tried to modify the track_ylab parameter but it don't allows to specify which tracks must ...
gtrellis written 19 months ago by Vinicius Henrique da Silva20
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Comment: C: DECIPHER version bug using biocLite()
... Hi Julian. Please check my update. I was unable to identify what was wrong with my versions.  ...
written 20 months ago by Vinicius Henrique da Silva20
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DECIPHER version bug using biocLite()
... I was trying to use the DECIPHER package today and it was not supporting even the examples in the manual. When I checked, I was using an old version (v 1.16.1). It was strange because I just installed it with: source("https://bioconductor.org/biocLite.R") biocLite("DECIPHER") Thus, I installed m ...
decipher written 20 months ago by Vinicius Henrique da Silva20
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Use matchPattern for large DNAStrings
... I would like to compare two DNAStrings that are larger than 20000 basepairs. I tried the matchPattern function from Biostrings package, however, I got this error: Error in .valid.algos(pattern, max.mismatch, min.mismatch, with.indels, : patterns with more than 20000 letters are not supported T ...
annotate biostrings written 21 months ago by Vinicius Henrique da Silva20 • updated 21 months ago by Hervé Pagès ♦♦ 13k

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Supporter 22 months ago, voted at least 25 times.

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