User: svlachavas

gravatar for svlachavas
svlachavas700
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700
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Trusted
Location:
Greece
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https://www.linkedin.c...
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15 hours ago
Joined:
5 years, 6 months ago
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s*********@eie.gr

Posts by svlachavas

<prev • 159 results • page 1 of 16 • next >
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Comment: C: How to select a "representative" transcript in multiple transcript variants from
... Dear GenoMax, thank you very much for your interesting suggestion- I have never heard it before-do you know or you have used it ? I could use gencode annotations, or you would go alternatively with selected gene symbols to check which are the most "representative" transcripts ? ...
written 1 day ago by svlachavas700
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Comment: C: How to select a "representative" transcript in multiple transcript variants from
... Dear Ram, thank you for your reply-unfortunately already I know the VEP option, we utilize ANNOVAR with an additional custom pipeline, thus we could not change in this current phase of the project ...
written 1 day ago by svlachavas700
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How to select a "representative" transcript in multiple transcript variants from annotation with ANNOVAR and gencode
... Dear Biostars, based on a recent annotation of resulted vcf files regarding the identification of somatic point alterations in a specific cancer of interest, I used ANNOVAR default settings with gencode annotation. Based on the relative output of files, I noticed the following pattern in a specific ...
annovar gencode transcript snp annotation written 1 day ago by svlachavas700
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Analyze RPPA cancer data in R for clustering patients and differential protein expression
... Dear Biostars, based on a current project I have acquired RPPA data based on selected proteins (metabolism and signaling networks) based on around ~1k patients with breast cancer. The major goal is both to cluster the patients into distinct groups and inspect the association with available clinicop ...
rppa de rppanalyzer clustering R written 3 months ago by svlachavas700
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Comment: A: how do I find the genes which are common to and those which differ between multi
... You can also check this very nice solution implemented in R: https://github.com/hms-dbmi/UpSetR which enables complex comparisons and nice visual representations ...
written 3 months ago by svlachavas700
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Filtering somatic point mutations and CNV alterations on the gene level for multi-omics data integration
... Dear Biostars community, based on an unsupervised approach for multi-omics data integration for detecting molecular subtypes in a specific cancer type, I have different omics layers for the same patients (360): rna-seq expression data, CNV and somatic point mutations. All of the different omics l ...
somatic mutations feature reduction multiomics written 3 months ago by svlachavas700
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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 11 months ago by svlachavas700
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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 11 months ago by svlachavas700
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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 12 months ago by svlachavas700
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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 12 months ago by svlachavas700

Latest awards to svlachavas

Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: how to get genes and their interactions from RNA-Seq data?
Appreciated 10 months ago, created a post with more than 5 votes. For A: TCGA - COAD read data gene expression analysis
Appreciated 13 months ago, created a post with more than 5 votes. For A: TCGA - COAD read data gene expression analysis
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: TCGA - COAD read data gene expression analysis
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 22 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 2.1 years ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: about microarray data analysis

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