Saifeldeen Mohamed's Projects
GenomeScratch is a user-friendly tool designed for generating virtual reference genomes, accompanied by GFF and GTF files. Tailored for testing workflows, it enables users to simulate genomic scenarios and optimize bioinformatics processes in a controlled, lightweight environment.
GeseqFold is a software tool devolped to process transcriptomic data and conduct differential gene expression analysis using the ordinary least squares (OLS) regression model.
mergeCounts is a user-friendly tool designed to effortlessly combine count matrices obtained after feature counting in RNA-seq pipelines. It efficiently merges these matrices into a unified format, facilitating downstream analyses.
Qiime 2, an advanced bioinformatics platform, specializes in analyzing metagenomic data. With a modular plugin architecture, integrated workflows, and visualization tools, Qiime 2 facilitates reproducible and transparent analyses, supporting both command-line and GUI interactions.
MOFA (Multi-Omics Factor Analysis) is a computational framework and statistical method designed for the integration and analysis of multi-omics data.
The provided set of bash scripts constitutes a comprehensive RNA-seq analysis workflow, facilitating the processing and analysis of high-throughput sequencing data.