User: Mithil Gaikwad

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Posts by Mithil Gaikwad

<prev • 12 results • page 1 of 2 • next >
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What can be done to separate the healthy and patient samples in PCA plot and Distance matrix
... Hello, I am doing RNA seq analysis to obtain Differential expression genes using DESeq2 for 13 patient and 6 Healthy donors. Before going for DESeq2 analysis, I am visualizing my samples by Distance matrix and PCA plot, using the following commands: library("RColorBrewer") sampleDistMatrix ...
visualization deseq2 pcaplot written 11 months ago by Mithil Gaikwad0 • updated 11 months ago by Michael Love26k
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Comment: C: tximport and its version
... Thank you very much it worked now, after installing newer version   ...
written 12 months ago by Mithil Gaikwad0
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Comment: C: tximport and its version
... Sorry, I didn't understand Can you please elaborate, What can I do to update my tools.   if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") Installing package into ‘/home/mithil/R/x86_64-pc-linux-gnu-library/3.4’ (as ‘lib’ is unspecified) Warning in insta ...
written 13 months ago by Mithil Gaikwad0
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tximport and its version
... Hello, I am usingtximport after StringTie quantification step, but I guess my tximport is not installed properly, because it is not accepting "stringtie" option and also not the none option: Is there any way to install tximport newer version or any other way. txi <- tximport(files, type = "stri ...
stringtie tximport rna-seq analysis written 13 months ago by Mithil Gaikwad0 • updated 13 months ago by James W. MacDonald52k
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Error while loading the data structrure in the ballgown tool
... Hello, I am facing an error while loading my data structure in ballgown tool,  I have triedfollowing are the commands which i am using in my data: >setwd("/Users/kchougul/data/testdata/Ballgown/tutorial_example") >library(ballgown) >library(ggplot2) >library(gplots) >library(genef ...
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Comment: C: GDC server down, try to use this package later
... Thank you Mr. Blighe But I am facing error in curl > devtools::install_github("BioinformaticsFMRP/TCGAbiolinks") Error in curl::curl_fetch_memory(url, handle = h) :   Failed to connect to api.github.com port 443: Connection timed out   What could be the problem? , I guess this error is becaus ...
written 13 months ago by Mithil Gaikwad0
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Can not install packages
... >install.packages("ballgown") Installing package into ‘/home/mithil/R/x86_64-pc-linux-gnu-library/3.4’ (as ‘lib’ is unspecified) Warning in install.packages :   package ‘ballgown’ is not available (for R version 3.4.4) > install.packages("genefilter") Installing package into ‘/home/mithil/R/x ...
genefilter ballgown rskittlebrewer written 13 months ago by Mithil Gaikwad0 • updated 13 months ago by Mike Smith4.0k
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Comment: C: Error in print.header("GDCquery: Searching in GDC database", "section") :could n
... > packageVersion("TCGAbiolinks") [1] ‘2.8.4’ > listSamples <- c("TCGA-E9-A1NG-11A-52R-A14M-07","TCGA-BH-A1FC-11A-32R-A13Q-07", +                  "TCGA-A7-A13G-11A-51R-A13Q-07","TCGA-BH-A0DK-11A-13R-A089-07", +                  "TCGA-E9-A1RH-11A-34R-A169-07","TCGA-BH-A0AU-01A-11R-A12P-07", ...
written 14 months ago by Mithil Gaikwad0
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Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header",
... I am facing the problem while running GDCquery in Rstudio using 'TCGAbiolinks' package stating that Error in print.header("GDCquery: Searching in GDC database", "section") :could not find function "print.header", while other function of GDC are running successfully like GDCDownload and GDCprepare, ...
dplyr tcgabiolinks dt written 15 months ago by Mithil Gaikwad0
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Comment: C: I am unable to use Rsubread. Thank you in advance.
... Thank you very much ...
written 15 months ago by Mithil Gaikwad0

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