User: lawarde.ankita1

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Posts by lawarde.ankita1

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Find Information about TCGA samples from GDC data portal
... Thank you so much for information and the reference. ...
written 6 months ago by lawarde.ankita130
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Find Information about TCGA samples from GDC data portal
... Hello Sir/ma'am, I have one question regarding the sample information from GDC (Genomic Data Commons) data portal. I am working on transcriptome profiling data of LUAD. My question is regarding to the drug treatments given to the patients. 1. when is the drug treatment given, before or after the s ...
tcga gdc sample information rna-seq written 6 months ago by lawarde.ankita130 • updated 6 months ago by svlachavas530
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Comment: C: Finding Mutation status of IDH1 from FireBrowse data
... Thank you for your suggestions. I really appreciate it. ...
written 6 months ago by lawarde.ankita130
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Difficulty in analysis of Differential gene expression of Firehose data
... Dear Sir/madam, I am working on LUAD data of gene expression, this data is RNA-SeqV2 RSEM normalized data. I want to find out the DEG between Tumor stage I and Stage IV. But im facing some problems, I'm using EBSeq package to find the DE genes, Below is the R code i have used (followed according t ...
R tcga rna-seq rsem ebseq written 8 months ago by lawarde.ankita130
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Comment: C: Analysing gene expression across clinical parameters
... Hi elizabethR, I am working on TCGA data of Lung cancer adenocarcinoma. Refereeing to your above question and the comments, as you said that you have used edgeR to perform differential expression analysis across clinical parameters, me also working on the same type of analysis. I want to find the D ...
written 8 months ago by lawarde.ankita130
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Not able to get DEG from FireBrowse data using R
... Hello everyone, I'm working on LUAD (Lung adenocarcinoma) data from FireBrowse. I want to find Differentially expressed genes according to the stage of the tumor. i have the clinical data with me and from that data i was able to take the samples which belongs to stage I(sub types a and b), Stage II ...
R rna-seq firebrowse deg written 8 months ago by lawarde.ankita130
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Finding Mutation status of IDH1 from FireBrowse data
... Hello everyone, I'm using GBM data from FireBrowse. I have RNAseq data downloaded from FireBrowse ( file name: GBM.rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.data) it has total 171 samples. I want to find the IDH1 mutations in the samples of GBM data. By follow ...
rnaseq mutation firebrowse written 8 months ago by lawarde.ankita130
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Comment: C: Differential Gene expression between low survival and high survival samples from
... Sorry to add this code as a separate comment, but the number of charcters in the post was exceeding than the 5000 Below is the code where i have followed TCGAbiolinks tutorial, library(TCGAbiolinks) library(DT) query.exp <- GDCquery(project = "TCGA-LUAD", ...
written 8 months ago by lawarde.ankita130
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Comment: C: Differential Gene expression between low survival and high survival samples from
... Hello roy.granit, here i provide with the R code i used for the DEG analysis usign edgeR, limma, #RNAseq- analysis, library(edgeR) library(limma) library(gplots) library(org.Hs.eg.db) #for annotations library(RColorBrewer) library(TCGAbiolinks) library(DT) quer ...
written 8 months ago by lawarde.ankita130
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Differential Gene expression between low survival and high survival samples from RNAseq
... Hello, I have one question regarding the approach of differential gene expression analysis from RNAseq data of cancer. Approach: 1) To find out the Defferentially Expressed Genes between low survived and high survived samples of patients. (example: here in my case, patients survived less than 1 ...
R deg survival rna-seq written 8 months ago by lawarde.ankita130

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