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Heraklion, Greece

Jason Charamis

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@JasonCharamis

Bioinformatician with 7 years experience in Computational and Comparative Genomics.

CWL-workflow-for-single-cell-RNAseq-analysis. CWL workflow for single-cell RNAseq data analysis using CellRanger or STARsolo. Performs initial steps from read trimming to generating the count matrix, as well as QC, normalization, feature selection, dimensionality reduction, clustering and marker gene detection.

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ARuS. Snakemake pipeline for running automated RNAseq analysis, from fastq reads to Differential Expression (DE) analysis. The latest version includes rules for post-DE annotation of genes, including annotation and/or orthology results.

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EGGNOG-functional-annotation-using-Snakemake. Snakemake workflow for functional annotation using eggNOG mapper v2

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SandFlyComparativeGenomics. Source code for the manuscript of Charamis et al. (2024)

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AVC. Shell

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PhyloSuite. Suite of tools that provide a unified framework of analyzing, manipulating and visualizing phylogenetic data.

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