User: Adam

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Adam0
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Poland
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7 months, 1 week ago
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1 year, 7 months ago
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Posts by Adam

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Select specific variants from vcf file
... Yes, actually I read about this package but don't you think it's a bit complicated? I'm asking becasue vcf file already has variation type, missense, splice region, frameshift etc. So maybe typical filter and grep from dplyr in R would be enough? ...
written 7 months ago by Adam0
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Select specific variants from vcf file
... Hello,   Does anyone know how to extract specific variants from vcf files? I have several vcf files with variants from NGS experiment, I'd like to subset only variants such as missense(stop gain stop loss, start gain, start loss)/splice site(in intron and exon) and all frameshift mutations. What ...
vcf written 7 months ago by Adam0 • updated 7 months ago by Martin Morgan ♦♦ 20k
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miRNA target prediction tool(package) using R
... Hello! I'm just curious, what tool are you use to get target for specific miRNA (given miRNA or sequence of totally novel molecue)? As I read here, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5187787/ there're plenty of packages for analysis such like this. Nevertheless, could you recommend me so ...
mirna prediction target written 8 months ago by Adam0
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Comment: C: Nice plot of gene region (plotTracks function)
... I get what I want finally, but I won't put it here. This page isn't for help others, is it? ...
written 9 months ago by Adam0
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Nice plot of gene region (plotTracks function)
... Hello I trying to make a nice plot such as in here: https://bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.pdf I mean, chromosome at the top and gene (I need only one gene) below, exons presetned as blocks and introns as line with arrows. My plot looks like this:   and m ...
gviz granges plottracks written 9 months ago by Adam0
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Answer: A: Methylation profile through chromosome
... Ok, with Assa Yeroslaviz help I've done what I need, nevertheless I'd like to share my solution, maybe it'll be useful for somebody. There are a few simple steps from simple '\t' separated file to nice visualization. 1. Install and load all stuff which will be needed. Data from my microarray was f ...
written 15 months ago by Adam0
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Comment: C: Methylation profile through chromosome
... Yes indeed this is what I'm looking for! However, have you done this before? Of course I'll try to convert it myself but let this topic to be open for possible further questions. Thank you :) ...
written 15 months ago by Adam0
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Methylation profile through chromosome
... Hello, I'm looking for some R package or even software to make methylation profile of chromosomes. I found two very nice packages for R: ChromHeatMap (plots made by this are what I'm looking for) quantsmooth Unfortunetaly my data isn't ExpressionSet or any object like this, so I don't know how to ...
R heatmap written 15 months ago by Adam0
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How to inteprate distances calculated by cmdscale?
... Hello, I have theoretical questions. I have differential gene expression data with values from 0 to 30000. I've calculated euclidean distances between probes in R. Mirror euclidean distance array has values between 0 and 5. Then I've used cmdscale method to gain points(probes) coordinates. Then I ...
differential gene expression mds cmdscale written 19 months ago by Adam0
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Is it possible to make some spheres around groups of points (plot3d) and measure distances between them?
... Hello, I'm looking for some clue, how to make nice spheres around my groups of pints and in addition make some lines between them and measure distances between them. I've made a 3d plot (plot3d) and distances were calculated by MDS method.     Groups are colored. I hope that easy solution for ...
rgl plot3d plotmds written 19 months ago by Adam0

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