User: svlachavas

gravatar for svlachavas
svlachavas610
Reputation:
610
Status:
Trusted
Location:
Greece/Athens/National Hellenic Research Foundation
Last seen:
1 day, 2 hours ago
Joined:
3 years, 6 months ago
Email:
s*********@eie.gr

I'm currently working as a PhD candidate at National Hellenic Research Foundation under the team of Metabolic Engineering & Bioinformatics, in Greece (http://www.eie.gr/nhrf/institutes/ibrb/programmes/metabolicengineering-en.html). My BSc Degree is in Molecular Biology and Genetics and my MSc Degree in Master’s Degree Program of Clinical Pharmacology and Therapeutics-Organized by the Medical School of the Democritus University of Thrace in collaboration with The Medical School of the University of Crete. My main interests focus on the development of computational & molecular methodologies empowering translational biomedical cancer research.

Posts by svlachavas

<prev • 458 results • page 1 of 46 • next >
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Comment: C: Implementation of specific cpm filtering in RNA-Seq data described in a previous
... Dear Gordon, thank you for your answer and clarifications-just a small comment, that i would like your opinion-despite not doing an edgeR DE analysis, you would agree that still filtering, even for using only the gene signature in downstream analysis, would still be initially beneficial for TMM nor ...
written 5 days ago by svlachavas610
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Comment: C: Implementation of specific cpm filtering in RNA-Seq data described in a previous
... Dear James, thank you for your suggestion-and I'm aware of the above function-however, as i have described in my previous link post, as i include only cancer samples, in the start there are not any pre-defined groups-only after downstream clustering, etc-thus, this function is not convinient in my p ...
written 5 days ago by svlachavas610
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Implementation of specific cpm filtering in RNA-Seq data described in a previously published edgeR pipeline
... Dear Community, i would like to ask a specific question concering a published paper with title : "It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR" (https://link.springer.com/protocol/10.1007%2F978-1-4939-3578-9_19) and th ...
rnaseq edger non-specific filtering cpm written 6 days ago by svlachavas610 • updated 5 days ago by Gordon Smyth34k
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Ok Aaron gotcha ...
written 6 days ago by svlachavas610
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Comment: C: Robust transformation of raw RNA-seq counts for exploratory data analysis and hi
... Dear Aaron, sorry to return again on this post, but i would like to add a very important question concering a published paper in which you are the author with title : "It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR" (htt ...
written 6 days ago by svlachavas610
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Comment: C: Error with R package motifbreakR while trying to read a vcf file with snps.from.
... Dear Valerie, thank you for your consideration on this matter-i have created also a post in the github account, but still i have not received an answer, as also from previous emails to the authors i did not get an answer, so i do not know if things are active-any custom solution you would support ? ...
written 10 days ago by svlachavas610
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Comment: C: Error with R package motifbreakR while trying to read a vcf file with snps.from.
... Dear Valerie, sorry to return again but this time, a new error appeared using the same exact code: snps.vcf <- snps.from.file(file=vcf_files,search.genome =BSgenome.Hsapiens.UCSC.hg38,format = "vcf") Error in info(snps) : could not find function "info" In addition: Warning message: In .bcfHeade ...
written 11 days ago by svlachavas610
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Answer: A: MultiAssayExperiment: how to store data for multiple cancer lesions for each pat
... Dear Mario,  have you checked the tutorial of the MultiAssayExperiment R package:  https://bioconductor.org/packages/release/bioc/vignettes/MultiAssayExperiment/inst/doc/QuickStartMultiAssay.html as also the quick cheatsheet arguments and functions: https://bioconductor.org/packages/release/bioc ...
written 21 days ago by svlachavas610
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Comment: C: Querying specific TCGA datasets through the MultiAssayExperiment R package
... Thank you Marcel for your updated answer-just an extra point that i forgot to mention for my answer-concering the data the MultiAssayExperiment containts, they are indeed hg19 correct ? And for the cox hazard model, if i find the same subset of genes with the hg19 analysis, significantly related wit ...
written 22 days ago by svlachavas610
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Comment: C: Querying specific TCGA datasets through the MultiAssayExperiment R package
... Dear Marcel, thank you for your quick comments and suggestions-just to recap and summarize some important comments based on your answer: 1) Yes, I'm a frequent user of TCGAbiolinks. mainly for analyzing transcriptomic and mutational data. However, for example there are various discrepancies when m ...
written 22 days ago by svlachavas610

Latest awards to svlachavas

Popular Question 12 months ago, created a question with more than 1,000 views. For (Gene-set)Pathway analysis based on network/pathway topology in R
Popular Question 12 months ago, created a question with more than 1,000 views. For Important r packages not available for R version 3.1.1
Popular Question 12 months ago, created a question with more than 1,000 views. For Problems importing Illumina raw data with lumi R package
Popular Question 12 months ago, created a question with more than 1,000 views. For Update R in Rstudio to specific version 3.2.1 in windows
Popular Question 12 months ago, created a question with more than 1,000 views. For Questions in limma about multifactorial design and possible batch effect correction
Popular Question 12 months ago, created a question with more than 1,000 views. For Correct assumptions of using limma moderated t-test
Student 12 months ago, asked a question with at least 3 up-votes. For Appropriate use of the function treat of the limma package
Popular Question 12 months ago, created a question with more than 1,000 views. For Error in PCA analysis and with ggbiplot function
Scholar 14 months ago, created an answer that has been accepted. For A: illuminaHumanv4.db : annotation source, and mapping to transcript names
Popular Question 16 months ago, created a question with more than 1,000 views. For Update R in Rstudio to specific version 3.2.1 in windows
Popular Question 16 months ago, created a question with more than 1,000 views. For Merge different datasets and perform differential expression analysis in limma
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Filtering on present/absent calls methodology and perfect match only arrays

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