User: svlachavas

gravatar for svlachavas
svlachavas600
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600
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Greece
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Posts by svlachavas

<prev • 140 results • page 1 of 14 • next >
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Perform correlation analysis between miRNA and mRNA expression data with different transformation values for the same samples
... Dear Community, based on a recent bioinformatics analysis of TCGA data, our goal is to perform correlation analysis in order to identify putative pairs of miRNA-mRNA expression pairs. In detail, based on rna-seq data, we have identified a small signature of 17 genes, as also 4 putative miRNA regula ...
tcga correlation analysis rna-seq mirna written 7 months ago by svlachavas600
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Comment: C: Appropriate bed files from library capture kit for computing on target coverage
... Thanks a lot Fin for the explanations !! Really appreciated it !! I will go for the exonic regions, as they are of main interest. Efstathios ...
written 11 months ago by svlachavas600
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Comment: C: Appropriate bed files from library capture kit for computing on target coverage
... Dear Fin, thank you for your comments-i have checked each file and the description in each-however, if the all_Tracks.bed is the same with the covered.bed, and the regions.bed is the same with the covered.bed, why there are created as different files ? and in the end, which specific file in your op ...
written 11 months ago by svlachavas600
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Comment: C: Appropriate bed files from library capture kit for computing on target coverage
... Sure Kevin, i just made a dropbox link with the compressed file from the above Agilent link: https://www.dropbox.com/s/8ulh1o8hcib0mms/S30409818_hs_hg38.zip?dl=0 ...
written 11 months ago by svlachavas600
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Appropriate bed files from library capture kit for computing on target coverage of WES bam files with Picard and CollectHsMetrics
... Dear Community, based on a WES project of cancer bam files for variant calling purposes, I'm currently trying to collect some specific quality metrics-namely the on target coverage for each bam file. Based on a small search, I found than Picard is capable of this analysis, through the following fun ...
picard on target coverage ngs wes bam files written 11 months ago by svlachavas600 • updated 11 months ago by finswimmer12k
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Comment: C: Group/Cluster tumor samples in an RNA-Seq dataset for survival analysis, based o
... Dear Kevin, thanks a lot for the detailed feedback and your suggestions-based on your ideas, in order to respond and ask some crusial questions on very specific points: A) Firstly, for your initial suggestion about the combined model with the glm function: if i have understood well, this approach ...
written 13 months ago by svlachavas600
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Group/Cluster tumor samples in an RNA-Seq dataset for survival analysis, based on the expression of a small gene signature
... Dear Community, based on a collaboration project, we have identified a small gene signature, discriminating relatively well control samples from tumor ones, based on an initial microarray analysis. The more important thing is that these genes, are also correlated with specific clinical imaging vari ...
R gene signature survival clustering rna-seq written 13 months ago by svlachavas600 • updated 13 months ago by Kevin Blighe51k
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Comment: C: Quality control issues for mRNA sequencing fastq files based on FastQC, based on
... Dear WouterDeCoster, of course i have read your very useful post, and also found this specific part-my mistake here, as i did not mention specifically my target goal of downstream analysis, in order for your answer to be more helpful: our goal, is to essentially test for the over- or under-represe ...
written 16 months ago by svlachavas600
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Comment: C: Quality control issues for mRNA sequencing fastq files based on FastQC, based on
... Thank you very much for your useful link-so, you think that downstream analysis is still feasible ? or you think it would be biased ? ...
written 16 months ago by svlachavas600
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Comment: C: Quality control issues for mRNA sequencing fastq files based on FastQC, based on
... Dear WouterDeCoster, still not ok ? ...
written 16 months ago by svlachavas600

Latest awards to svlachavas

Teacher 27 days ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: how to get genes and their interactions from RNA-Seq data?
Scholar 10 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Voter 19 months ago, voted more than 100 times.
Centurion 19 months ago, created 100 posts.
Scholar 23 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Scholar 24 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Supporter 3.1 years ago, voted at least 25 times.

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