User: Björn

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Björn30
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Posts by Björn

<prev • 77 results • page 1 of 8 • next >
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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 6 days ago by Björn30
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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 ! ...
pca edger heatmaps written 7 days ago by Björn30
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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 10 days ago by Björn30
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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 10 days ago by Björn30
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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 10 days ago by Björn30 • updated 10 days ago by toralmanvar420
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Comment: A: How to find patient sample.type in TCGA-PRAD ?
... The clinical- patient data, the bcr_patient_barcode contains only "TCGA-HC-A6AP" (without 01A) unlike in transcriptome data. So, from the list of clinical data, how to know sample.type. This was my question. ...
written 21 days ago by Björn30
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How to find patient sample.type in TCGA-PRAD ?
... Hi, I downloaded clinical- patient data for TCGA-PRAD. Following are the colnames colnames(cli_patient) [1] "bcr_patient_barcode" "additional_studies" [3] "tumor_tissue_site" "other_dx ...
tcgabiolinks sample.type clinical.patient written 26 days ago by Björn30
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Comment: A: How to link "miRNA gene quantification" and "clinical- Patient" data retrieved f
... Kevin Blighe, Thank you so much for taking time to explain in details. I really appreciate that For first query, I used following commands names(file.csv)<-substring(names(file.csv),1,12) colnames(file.csv)[1]<-file.csv("miRNA") write.csv(file.csv, "newfile.csv",row.names = F) Thi ...
written 4 weeks ago by Björn30
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How to link "miRNA gene quantification" and "clinical- Patient" data retrieved from TCGA
... The query below is too much details but might be simple to answer for experienced ones. I spent lots of time to figure out but came to conclusion that I need help from experts. I downloaded "miRNA gene quantification" from TCGA harmonized data which I saved as CSV file. This data set is more like ...
contrast tcga mirnaseq edger written 4 weeks ago by Björn30
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Comment: C: Why "Parse XML clinical data" in TCGAbiolinks gives error in Rstudio ?
... Thanks,I have nearly 600 individual xml files in individual folders which is standard download from TCGA. So, no idea how to sort it out? ...
written 4 weeks ago by Björn30

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