User: svlachavas

gravatar for svlachavas
svlachavas680
Reputation:
680
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Trusted
Location:
Greece
Website:
https://www.linkedin.c...
Last seen:
3 weeks, 3 days ago
Joined:
4 years, 12 months ago
Email:
s*********@eie.gr

Posts by svlachavas

<prev • 153 results • page 1 of 16 • next >
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Comment: C: Possible approach to select normal tissue samples for cancer RNA-Seq data withou
... Dear ATpoint, thank you for your strong point- to be honest, i did not participate in any prior experimental design of the project, and I was implicated after the creation of the data. Unfortunately, these are some older data, that's why as I very recently got into the analysis and any relative inf ...
written 4 months ago by svlachavas680
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Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
... Dear Community, based on a clinical project of high-throughput genomics data, we have gathered a high number of RNA-Seq samples from patients with different solid tumors, that have undergone conventional therapy prior sequencing. All the data have been uniformly processed through R. The major issue ...
R de rna-seq gtex batch effect written 4 months ago by svlachavas680
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Comment: C: Survival analysis with gene expression
... Dear Kevin, thank you very much for your answer !! do you think that based on the experimental design of this dataset-that is the majority of the patients have undergone initial therapy-RFS would be a more "robust" estimate of survival,as essentially if measuring overall survival, is more related t ...
written 5 months ago by svlachavas680
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Answer: A: normalization after merging datasets
... Initially, as Jared mentioned, you should provide detailed information about your experimental design and biological question, without just explicitly posting some code chunks, as others will be more willing and able to help you. In conjunction with the above answers, you might also want to check t ...
written 5 months ago by svlachavas680
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Comment: A: Survival analysis with gene expression
... Dear Kevin, excellent and comprehensive tutorial as always !! I have three quick questions regarding the implementation of your tutorial: briefly, based on the TCGA-GDC RNA-Seq dataset of breast cancer, i have identified a very small number of genes (~5) with significant differences in overall survi ...
written 5 months ago by svlachavas680
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Answer: A: Best way for CNV phenotype association analysis.
... Dear Keremwai, based on your description and project, I would suggest the R package CNVRanger, which provides various functionalities for CNV analysis, including a CNV-phenotype association pipeline, with a very comprehensive vignette: https://doi.org/10.1093/bioinformatics/btz632 https://biocond ...
written 5 months ago by svlachavas680
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Comment: C: Suggested tool or algorithm for accessing pathogenicity and prioritization of so
... Dear Collin, thank you for your suggestions-I will definitely take a detailed look regarding CHASMplus-by missense mutations, you are referring to SNPS right ? thus, these methodologies might be helpful for prioritization of somatic point mutations... Additionally, we are definitely interested in ...
written 6 months ago by svlachavas680
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Suggested tool or algorithm for accessing pathogenicity and prioritization of somatic INDELs in cancer research
... Dear All, I would like to ask if there is a pathogenicity or deleteriousness score implemented in any tool, regarding the process of somatic variant annotation, that could be used specifically in the case of putative somatic insertions/deletions, derived from the analysis of WGS/WES cancer data ? A ...
somatic variant annotation pathogenicity cancer written 6 months ago by svlachavas680
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Suggestion of specific tools/pipelines for the manipulation and analysis of VCF files after somatic copy number variant calling
... Dear Community, briefly, implementing a somatic Copy Number Variant Calling using the cnv_facets command line tool, based on the original FACETS algorithm, resulted in a number of VCF files with the final CNAs. My main issue is regarding the manipulation of these vcf files: 1) to filter the VCF fi ...
vcf cna cnv facets vcf analysis written 6 months ago by svlachavas680
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Suggested pipeline to perform variant calling for cancer exome sequencing samples of PDX models
... Dear Community, I would like to ask a methodological question regarding a specific scenario for somatic variant calling concerning whole exome sequencing data: briefly, based on a biological protocol regarding the isolation of circulating tumor cells (CTCs) from patients with lung cancer, in vivo ...
variant calling pdx wes liquid biopsy written 6 months ago by svlachavas680 • updated 3 months ago by akshayb0420

Latest awards to svlachavas

Appreciated 3 months ago, created a post with more than 5 votes. For A: TCGA - COAD read data gene expression analysis
Appreciated 6 months ago, created a post with more than 5 votes. For A: TCGA - COAD read data gene expression analysis
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: TCGA - COAD read data gene expression analysis
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 15 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 19 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Voter 2.3 years ago, voted more than 100 times.
Centurion 2.4 years ago, created 100 posts.

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