Mahmoud Ahmed

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Using cRegulome
Package Vignette: Transcription factors and microRNAs are important for regulating the gene expression in normal physiology and pathological conditions. Many bioinformatic tools were built to predict and identify transcription factors and microRNA targets and their role in development of diseases including cancers. The availability of public access high throughput data allowed for data-driven discoveries and validations of these predictions. Here, we build on that kind of tools and integrative analyses to provide a tool to access, manage and visualize data from open source databases. cRegulome provides a programmatic access to the regulome (microRNA and transcription factor) correlations with target genes in cancer. The package obtains a local instance of Cistrome Cancer and miRCancerdb databases and provides objects and methods to interact with and visualize the correlation data.
Case Study
Package Vignette: In this brief study, we attempted to answer questions raised by Shi and colleagues in a paper published in PLOS in 2015. The aim of this case study is to illustrate the use of `cRegulome` to obtain data based on queries of interest. Secondly, to integrate the package in a useful and meaningful workflow and give a context to the kind of information one can get from such databases.
Analysis of real-time qPCR data
Package Vignette: Quantitative real-time PCR is an important technique in medical and bio-medical applications. The `pcr` package provides a unified interface for quality assessing, analyzing and testing qPCR data for statistical significance. The aim of this document is to describe the different methods and modes used to relatively quantify gene expression of qPCR and their implementation in the `pcr` package.
Meta-analyses Workflow
Meta-analysis of effect o BCG vaccine on Tuberculosis test outcomes
Prediction App
A demo mata-analysis of the relation between BCG vaccine and Tuberculosis test outcomes
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BMI Application
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Storm Data analysis
Assignment for Reproducible Research course