User: Björn

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Björn40
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Posts by Björn

<prev • 92 results • page 2 of 10 • next >
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what to use in "Geneinfo" for miRNA in -TCGAanalyze_Normalization- of TCGAbiolinks
... Hi, For **mRNA** DE expression, the code used is dataNorm <- TCGAanalyze_Normalization(tabDF = dataPrep, geneInfo = geneInfo, method = "gcContent") However, what should I use for miRNAs in dataNorm <- TCGAa ...
normalization tcga mirna geneinfo written 22 months ago by Björn40
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(Closed) How to link non-unique colnames in two different files ?
... I have a file1 with example col names as follows *xyz-123 xyz-234 abc-345 abc-789*. Another file2 with row names *xyz abc*. How to link file2 and file1 using row names of file2. Please note *xyz-123 xyz-234* have different information from same patient. I need to link those files and process into ...
R dplyr written 22 months ago by Björn40
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Answer: A: Is miRNA microarray better than NGS for circulating miRNA quantification?
... It all depends on your research question. For targeted approach, microarray will be better and cheaper than NGS. You mentioned that you are using advanced AI, then probably you can try TCGA data. ...
written 22 months ago by Björn40
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How to decode patient barcode inTCGA database ?
... Following the command below query <- GDCquery(project = "TCGA-PRAD", data.category = "Clinical",file.type = "xml") GDCdownload(query) clinical.radiation <- GDCprepare_clinic(query, directory = "GDCdata", clinical.info = "patient") I downloaded the data in CSV fi ...
R tcga patient gdc written 22 months ago by Björn40 • updated 20 months ago by zx87549.2k
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Comment: C: How to make circos plot in R for miRNA and target genes retrieved from targetsca
... @toralmanvar, My question was about input data required for such Circos graph. I have lists of miRNAs and target genes from target scan. Now, what additional data do I need before I proceed. Thanks ...
written 22 months ago by Björn40
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Comment: C: How to create PCA plot and heatmaps using only significant genes in edgeR ?
... Thanks Kevin, I used standard edgeR code for PCA but wanted to create PCA for 50 DE genes out of 2000. Use only 50 genes out of 2000 in PCA plot. ...
written 23 months ago by Björn40
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How to create PCA plot and heatmaps using only significant genes in edgeR ?
... How to create PCA plot and heatmaps using only significant genes in edgeR ? I have 10 genes at signficant different levels between comparison groups. How can I create PCA and heatmaps with only those 10 genes. Suggestions on R code will be appreciated ! ...
R pca edger heatmaps written 23 months ago by Björn40 • updated 20 months ago by zx87549.2k
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Comment: C: How to make circos plot in Rstudio for miRNA and target genes retrieved from tar
... Hi Sej, Thanks for your comment. Can you suggest me the input data to create such plots Thanks in advance ...
written 23 months ago by Björn40
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Comment: C: How to make circos plot in Rstudio for miRNA and target genes retrieved from tar
... I would like to prepare a plot similar to **Figure 2-Circos plot between the three predicted miRNAs and their targets**. of this paper doi: 10.1016/j.gdata.2015.09.005 [paper][1] I have 10 miRNAs and respective predictive genes from TargetScan. What are the input data to create circos plots. e.g. ...
written 23 months ago by Björn40
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How to make circos plot in R for miRNA and target genes retrieved from targetscan?
... How to make circos plot in **R** for miRNA and target genes retrieved from targetscan ? Out of many genes, is there a way to filter out only significant target genes. I believe there must be a scientific reasoning for it. Any hands-on tutorial documents or reference would be appreciated. ...
circos plot genes mirna targetscan R written 23 months ago by Björn40 • updated 23 months ago by toralmanvar840

Latest awards to Björn

Popular Question 20 months ago, created a question with more than 1,000 views. For rnaseq sequence analysis and trimming
Popular Question 20 months ago, created a question with more than 1,000 views. For rnaseq sequence analysis and trimming
Popular Question 21 months ago, created a question with more than 1,000 views. For How to cluster in heatmap.2
Popular Question 21 months ago, created a question with more than 1,000 views. For rnaseq sequence analysis and trimming

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