User: svlachavas

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svlachavas520
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Greece
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https://www.linkedin.c...
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an hour ago
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3 years, 3 months ago
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Posts by svlachavas

<prev • 136 results • page 1 of 14 • next >
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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 1 hour ago by svlachavas520
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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 9 weeks ago by svlachavas520
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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 10 weeks ago by svlachavas520 • updated 9 weeks ago by Kevin Blighe33k
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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 5 months ago by svlachavas520
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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 5 months ago by svlachavas520
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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 5 months ago by svlachavas520
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Quality control issues for mRNA sequencing fastq files based on FastQC, based on Per Base Sequence Content
... Dear Community, i would like to ask some comments and suggestions concerning the interpretation of some initial quality control results of fastq files. In detail, in a current RNA-Seq project for gene expression data, based on 2 different cancer cell lines, mRNA sequencing was performed for 12 sam ...
mrnasequencing sequence rna-seq fastqc written 5 months ago by svlachavas520 • updated 5 months ago by WouterDeCoster35k
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Comment: C: customized clusterAlg of NMF in consensusClusterPlus
... Dear sugus, just from curiosity, i saw your very interesting post and implementation with NMF-did you got any "biologically" interesting or robust results with your above implementation ? I'm mainly asking because I'm also frequently using ConsensusClusterPlus for unsupervised class discovery in ca ...
written 5 months ago by svlachavas520
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Comment: C: Implementation of the COSMIC database for somatic variant annotation and filteri
... Thanks Kevin for the updates-concerning my current project and specific goal of analysis: we have for an initial number of 3 patients both whole exome sequencing data ( Small Cell Lung Cancer-Genomic DNA captured using Agilent in-solution enrichment methodology/paired-end 75 bases massively paral ...
written 5 months ago by svlachavas520
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Comment: C: Implementation of the COSMIC database for somatic variant annotation and filteri
... Dear Kevin, thank you very much for your comprehensive answer and comments-just some thoughts based on your suggestions- 1) So in your opinion, even though i have WES data, i should download the COSMIC Mutation Data, based on various points such as your the 5' and 3' UTR regions right ? even thoug ...
written 5 months ago by svlachavas520

Latest awards to svlachavas

Teacher 8 weeks 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
Voter 7 months ago, voted more than 100 times.
Centurion 8 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Scholar 13 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Supporter 2.2 years ago, voted at least 25 times.
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Scholar 3.2 years ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor

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