Repository for RNA-seq and microarray pipelines

This git repository includes RNA-seq data analysis pipelines, protocols, strategies, figures, and supplemental information of peer-reviewed manuscripts.

Licence: MIT Licence

Language prerequisites

Shell/bash, Python, R, MySQL, D3.js

Genetic analyses and published projects

1. Repository of automated sequence analyses, statistics, and machine learning on high performance clusters (Bassim 2013-2018)
2. Supervised learning with gene expression data including multiclustering and genetic networks at the University Health Network (Bassim 2018) PDF
3. Networks of a cross-talk between host and pathogenic parasite with dual RNA-seq at the New York University (Bassim 2017) PDF
4. Difference in networks between neural and respiratory cells with RNA-seq data at the New York University (Bassim 2016) PDF
5. Hotspots for variants in pathogenic parasite with RNA-seq data at the New York University (Bassim 2015) PDF
6. Functional domain curated databases for gene annotation (Bassim 2015) best used with the automated aggregation of gene metadata script (Bassim 2017)
7. Descriptive analysis between algae species at the New York University (Bassim 2015)
8. Variant annotation and frequency in Parkinson’s disease from clinical data at the University of Vermont (Bassim 2015) PDF
9. Brain disease repository including databases and workflows at the University of Vermont (Bassim 2015)
10. Aggregated bibliographies in machine learning, deep learning, brain disease methods, and non-model species bioinformatics
11. Bassim PhD thesis involving microarray analyses, Bayesian networks, clustering, and machine learning at the University of Quebec (Bassim 2014)

Relevant material

Subject	Repo	Code	Author	Year
Statistical learning	Summary		S. Bassim	2013
Blast+		shell	S. Bassim	2015
Linux special addons	Table		S. Bassim
Linux configurations	Software		S. Bassim	2015
D3.js summary		javascript	S. Bassim
R summary functions	Table		S. Bassim
Emacs key-bindings	Table		S. Bassim
Archlinux configs		shell	S. Bassim

Author mentions

• Empirical Bayes Estimation of Dynamic Bayesian Networks (ebdbNet) on CRAN (updates).
• Google Scholar personal page for published papers.
• Linkedin profile for ongoing projects.
• Research gate personal page for downloading published papers.
• Discovery of new PPAR target genes in the glioblastoma cell line T98G Oncology