User: shivangi.agarwal800

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Posts by shivangi.agarwal800

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Comment: C: Installing Genomicdatacommon in r
... Resolved the above error by installing the package in R 3.5, but got another error. I followed the commands in Kevin post, all commands ran successfully, but when I was running on my file, it gave error, I ran the commands as : > library(GenomicDataCommons) > > manifest <- read.table(" ...
written 8 weeks ago by shivangi.agarwal80040
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Answer: A: Installing Genomicdatacommon in r
... For matching file id with TCGA barcodes, I am following Kevin post "Question: problem in matching the names between file names and patients Id in TCGA" https://www.biostars.org/p/318756/#318919 But getting error. Kindly suggest Regards Shivangi ...
written 8 weeks ago by shivangi.agarwal80040
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Comment: C: Installing Genomicdatacommon in r
... Thanks for your reply. No, there is nothing like that. All other things are working fine. ...
written 8 weeks ago by shivangi.agarwal80040
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Answer: A: Obtaining the CNA data
... Hi While unzipping TP.CopyNumberLowPass_Gistic2.aux.2016012800.0.0.tar.gz, there is GDAC_Gistic2Report_22529547_broad_data_by_genes.txt file. While looking into the contents, I got as GDAC_Gistic2Report_22529547_broad_data_by_genes.txt | cut -f-15 Gene Symbol Locus ID Cytoband TCGA-3C-AAAU-01A-11D ...
written 8 weeks ago by shivangi.agarwal80040
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Installing Genomicdatacommon in r
... Hi I am installing GenomicDataCommons in R, but when giving following command, getting error as: GenomicDataCommons::status() Error in curl::curl_fetch_memory(url, handle = handle) : Could not resolve host: gdc-api.nci.nih.gov Kindly suggest. Thanks in advance With regard ...
genomicdatacommon written 8 weeks ago by shivangi.agarwal80040 • updated 8 weeks ago by Vijay Lakhujani3.5k
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Comment: C: Obtaining the CNA data
... Have edited the original question ...
written 8 weeks ago by shivangi.agarwal80040
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Comment: C: Obtaining the CNA data
... I downloaded the data from Gistic and Cosmic, but I didnot get the data in the form I want. I want the data cancerwise, patientwise and genewise, like we get the expression data. From Gistic, I downloaded different files as: gdac.broadinstitute.org_BRCA-TP.CopyNumberLowPass_Gistic2.mage-tab.2016012 ...
written 8 weeks ago by shivangi.agarwal80040
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Obtaining the CNA data
... Hi I want to obtain the CNA data for particular cancer type. I downloaded the data from Gistic and Cosmic, but I didnot get the data in the form I want. I want the data cancerwise, patientwise and genewise, like we get the expression data. From Gistic, I downloaded different files as: gdac.broadi ...
cna cancer written 8 weeks ago by shivangi.agarwal80040
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Query regarding TCGA samples
... Hi I want to look into the mutation profile of tumor samples obtained from TCGA. Looking deep into the sample barcodes, I found that the analyte codes of different samples are different, for e.g. Here is three sample ids from same study, but there analyte is different. > TCGA-A7-A0DB-01A-11**D ...
samples tcga written 11 weeks ago by shivangi.agarwal80040 • updated 11 weeks ago by Kevin Blighe35k
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Comment: C: Mutational landscape plot
... Hi I noticed one problem while plotting this plot. When I simply plotted data given [in the link][1], I noticed that the gene which is having two same types of mutation with different variant in the same sample is being shown in the plot only once. example, the gene MAP3K1 is having two frame shift ...
written 3 months ago by shivangi.agarwal80040 • updated 11 weeks ago by RamRS20k

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