User: svlachavas

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svlachavas560
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Greece
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https://www.linkedin.c...
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3 years, 10 months ago
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s*********@eie.gr

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 8 weeks ago by svlachavas560
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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 5 months ago by svlachavas560
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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 5 months ago by svlachavas560
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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 5 months ago by svlachavas560
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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 6 months ago by svlachavas560 • updated 5 months ago by finswimmer11k
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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 8 months ago by svlachavas560
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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 8 months ago by svlachavas560 • updated 8 months ago by Kevin Blighe43k
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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 11 months ago by svlachavas560
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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 11 months ago by svlachavas560
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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 11 months ago by svlachavas560

Latest awards to svlachavas

Scholar 5 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Voter 13 months ago, voted more than 100 times.
Centurion 14 months ago, created 100 posts.
Scholar 18 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Scholar 19 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Supporter 2.7 years ago, voted at least 25 times.
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Scholar 3.7 years ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor

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