User: Jack

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Jack40
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Posts by Jack

<prev • 19 results • page 1 of 2 • next >
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Generate Gene plot for region on hg19
... So, given a matrix from the HumanGenome19 project (hg19) I want to generate a plot in which I the genes and their strands will be plotted. The data from hg19 look like this: GENE CHR txStart txEnd Size STRAND RBBP8 chr18 2050000 42016610 113940 - CCND3 chr18 41902670 42016610 113940 - ...
R genes plot written 4 weeks ago by Jack40 • updated 4 weeks ago by krushnach8080
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Plot SNPs on GViz
... I have a list of snps in .txt format. only 10 snps to be exact, that appear on a certain region on chromosome 7. In my text file, I have the position of the SNP and the values I need, I just have to create the `zoomed-in` effect like in the picture below. I 'm using GViz, to plot the Ideogram of th ...
R snps gviz written 6 weeks ago by Jack40
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Comment: C: Remove text labels of variables on diagonal corrplot
... @ddiez I've updated the question. check it again. ...
written 6 weeks ago by Jack40
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Remove text labels of variables on diagonal corrplot
... How can I remove text labels from diagonal only on corrplot? my_correlation_matrix1 <- read.table("path/to/matrix", header = T) my_correlation_matrix2 <- read.table("path/to/matrix", header = T) corrplot(my_correlation_matrix1, method = "color", ...
R corrplot written 6 weeks ago by Jack40 • updated 6 weeks ago by ddiez1.4k
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Answer: A: Get hg19 coordinates of SNPs from gwas catalog
... have a look at [this][1] . at least for my project, I found what I needed. [1]: http://www.nature.com/ncomms/2015/150122/ncomms6966/extref/ncomms6966-s3.xlsx ...
written 6 weeks ago by Jack40
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Answer: A: Plot a DNA chain in R
... The answer is Gviz library and Ideogram ...
written 6 weeks ago by Jack40
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Comment: C: Plot a DNA chain in R
... @Im687 wow! Thank you! this just might be it! ...
written 6 weeks ago by Jack40
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Plot a DNA chain in R
... Hello, I'm kinda new to this, what I would like to do is plot a DNA chain in R. Namely: A thick `vertical line` that will represent one DNA chain, and next to it I want to put some `zoom-in` windows that will highlight specific positions on it. Can I do this in R? Or do I need another software? ...
R dna plot written 6 weeks ago by Jack40
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Get CMap data
... Is there an R package that would take Broad Institutes CMap data and organize them in pathways? My colleagues are confident that there is one but they dont remember the name. ...
institute cmap broad written 8 weeks ago by Jack40 • updated 8 weeks ago by Zhilong Jia1.0k
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What libraries to use for Broads Cmap?
... I would like to start using CMap from Broad, but I don't know how to use it. Are there any specific tutorials that I should watch? or specific R (or Python) packages to download? More specifically, I would like to try to identify compounds in CMap that are either up- or down-regulated. ...
up-regulated cmap broad down-regulated written 10 weeks ago by Jack40 • updated 10 weeks ago by igor3.4k

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