User: svlachavas

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svlachavas640
Reputation:
640
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Greece
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https://www.linkedin.c...
Last seen:
14 hours ago
Joined:
4 years, 6 months ago
Email:
s*********@eie.gr

Posts by svlachavas

<prev • 148 results • page 1 of 15 • next >
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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 15 hours ago by svlachavas640
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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 4 days ago by svlachavas640
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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 ...
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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 23 days ago by svlachavas640
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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 29 days ago by svlachavas640
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Comment: C: Estimate tumor purity for liquid cancer biopsy samples of whole exome sequencing
... Dear Amjad, thank you for the additional description-thus far, as i don't have any ctDNA samples, the second scenario would suit. Currently, all the samples (both biopsies and CTCs) are at the time of diagnosis, prior therapy. Thus, i have used tools like FACETS to get an estimation of tumor purity ...
written 4 weeks ago by svlachavas640
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Comment: C: Estimate tumor purity for liquid cancer biopsy samples of whole exome sequencing
... Dear Amjad, thank you for your suggestion and idea. Just two relative questions on this matter-your R package is designed only for circulating tumor DNA, and not for biopsies, correct ? Moreover,what particular analyses your pipeline implements, and I would benefit specifically if I analyzed the C ...
written 4 weeks ago by svlachavas640
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Estimate tumor purity for liquid cancer biopsy samples of whole exome sequencing data
... Dear Community, briefly, in a current collaboration project, i have performed variant calling analysis on cancer whole exome sequencing data on a small number of 4 patients with small cell lung cancer (Circulating tumor cells sample, biopsy cancer sample and the relative peripheral blood normal sa ...
variant calling liquid biopsy wes tumor purity written 9 weeks ago by svlachavas640 • updated 4 weeks ago by amjad80
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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 10 months ago by svlachavas640
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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 14 months ago by svlachavas640

Latest awards to svlachavas

Appreciated 23 days ago, created a post with more than 5 votes. For A: TCGA - COAD read data gene expression analysis
Good Answer 23 days ago, created an answer that was upvoted at least 5 times. For A: TCGA - COAD read data gene expression analysis
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 9 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 13 months ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: about microarray data analysis
Voter 22 months ago, voted more than 100 times.
Centurion 22 months ago, created 100 posts.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Transcriptome Analysis Console (TAC) vs R Bioconductor

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