This git repository includes RNA-seq data analysis pipelines, protocols, strategies, figures, and supplemental information of peer-reviewed manuscripts.
Licence: MIT Licence
Shell/bash, Python, R, MySQL, D3.js
- Repository of automated sequence analyses, statistics, and machine learning on high performance clusters (Bassim 2013-2018)
- Supervised learning with gene expression data including multiclustering and genetic networks at the University Health Network (Bassim 2018) PDF
- Networks of a cross-talk between host and pathogenic parasite with dual RNA-seq at the New York University (Bassim 2017) PDF
- Difference in networks between neural and respiratory cells with RNA-seq data at the New York University (Bassim 2016) PDF
- Hotspots for variants in pathogenic parasite with RNA-seq data at the New York University (Bassim 2015) PDF
- Functional domain curated databases for gene annotation (Bassim 2015) best used with the automated aggregation of gene metadata script (Bassim 2017)
- Descriptive analysis between algae species at the New York University (Bassim 2015)
- Variant annotation and frequency in Parkinson’s disease from clinical data at the University of Vermont (Bassim 2015) PDF
- Brain disease repository including databases and workflows at the University of Vermont (Bassim 2015)
- Aggregated bibliographies in machine learning, deep learning, brain disease methods, and non-model species bioinformatics
- Bassim PhD thesis involving microarray analyses, Bayesian networks, clustering, and machine learning at the University of Quebec (Bassim 2014)
| 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 |
- 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