User: chetana

gravatar for chetana
chetana40
Reputation:
40
Status:
New User
Location:
San Diego
Last seen:
3 months ago
Joined:
2 years, 1 month ago
Email:
c************@gmail.com

Posts by chetana

<prev • 22 results • page 1 of 3 • next >
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Retrive orthologs for coral housekeeping genes
... Hi, I have a list of genes named beta-actin, ribosomal protein L12 and Ploy(a) binding protein. These genes under any condition tend to be stable in cnidaria and hence can be used as candidate genes to normalize gene expression data (http://www.sciencedirect.com/science/article/pii/S0165022X0700156 ...
gene database written 4 months ago by chetana40
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Comment: A: Conditionally coloring the fold change values to plot a heatmap using pheatmap
... Please find the code below. Patterns are the way set of few genes fall into a category based on their expression across the timepoints and I just used it for the row annotation. library(pheatmap) library(RColorBrewer) geneExp <- read.table("ICL004-R_Pattern1-10.txt", ...
written 9 months ago by chetana40
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Conditionally coloring the fold change values to plot a heatmap using pheatmap
... Hi all, I'm trying to plot a heat map with fold change (log2 values) values ranging from almost -100 to 100 across 6 time points. There are actually very few points in the extreme ranges of fold change. I was planning on plotting just the -10 to 10 range in the scale with differing color intensity ...
bioinformatics heatmap R written 9 months ago by chetana40
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Comment: C: How to import both node and edge files into cytoscape from WGCNA?
... Are you using desktop version of Cytoscape? If so is it MAC or windows? ...
written 11 months ago by chetana40
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Comment: C: RShiny interactive volcano plots
... Hi Jacob, it worked. Thank you so much. ...
written 11 months ago by chetana40
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Comment: A: RShiny interactive volcano plots
... `ui <- fluidPage( titlePanel("Volcano Plotly"), fluidRow( column( width = 10, plotlyOutput("volcanoPlot", height = "500px") ), column( width = 8, dataTableOutput("selectedProbesTable") ) ) ...
written 12 months ago by chetana40
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Comment: C: RShiny interactive volcano plots
... Thanks for your reply Steve and sorry if I was not clear asking the question. Here I include the headers of the dataframe as an example as the data is really huge. ***probe gene_symbol Timepoint0_FC Timepoint0_P Timepoint3_FC Timepoint3_P Timepoint7_F Timepoint7_P*** Here FC is the foldchange ...
written 12 months ago by chetana40
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Comment: C: RShiny interactive volcano plots
... I'm happy to explain, Michael. Bioinformatics is an interdisciplinary field and according to me if we're trying to solve a biological problem with a programmatic approach I consider it to be a bioinformatics problem. Since I'm working with biological data/ expression data I think it is relevant to c ...
written 12 months ago by chetana40
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RShiny interactive volcano plots
... Hi everyone, I'm a newbie to Rshiny and I'm trying to make a Rshiny app using this link mentioned here ([https://bioinformatics-core-shared-training.github.io/shiny-bioinformatics/interactive-plots][1]), it uses ggplot+plotly to make the plot interactive. I want to try it on my timepoint data and h ...
R rshiny differential expression bioinformatics written 13 months ago by chetana40 • updated 12 months ago by h.mon21k
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Comment: C: WGCNA: Error plotting TOM
... It's a cluster that I'm running it on and RAM is around 160GB. ...
written 16 months ago by chetana40

Latest awards to chetana

Popular Question 7 months ago, created a question with more than 1,000 views. For RNA Seq data network analysis
Popular Question 7 months ago, created a question with more than 1,000 views. For Retrieve species name using taxaIDs of NCBI

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