- T-tests
- Volcano plot
- One-way Analysis of Variance (ANOVA)
- Correlation Analysis
- Pattern Searching
- Chemometrics Analysis
- Principal Component Analysis (PCA)
- Partial Least Squares - Discriminant Analysis (PLS-DA)
- Sparse Partial Least Squares - Discriminant Analysis (sPLS-DA)
- Orthogonal Partial Least Squares - Discriminant Analysis (orthoPLS-DA)
- Feature Identification
- Significance Analysis of Microarray (and Metabolites) (SAM)
- Empirical Bayesian Analysis of Microarray (and Metabolites) (EBAM)
- Cluster Analysis
- Hierarchical Clustering: Dendrogram/Heatmaps
- Partitional Clustering: K-means/Self Organizing Map (SOM)
- Classification & Feature Selection
- Random Forest/Support Vector Machine (SVM) /Pathway analysis/Pathway Topology Analysis /Over Representation Analysis
- Biomarker analysis
- Classical univariate ROC curve analyses
- Multivariate ROC curve based exploratory analysis (Explorer)
- ROC curve-based model evaluation (Tester)
- Enrichment analysis with network view
5. Tools for managing large amounts of data
- Version-control systems: GitHub/Harvard Dataverse/Zenodo/Dat. Recording entire data workflow with video-capture tool asciinema and meta-data with README/JSON
- Automation tools (Apache Spark and Apache Hbase) to validate data-quality assurance steps. Self-contained computing environment-Docker container / online platform Code Ocean/ Binder/Gigantum/Nextjournal
- Tools to create documents that combine software code, text, and figures: Jupyter Notebook/ Terra/Seven Bridges Genomics. Stack Overflow/The Carpentries helping resources
- Working knowledge of databases and Structured Query Language (SQL)/Linux command line
- Familiarity with AWS/GCP cloud-computing services (e.g., Storage & Databases/Virtual machines/CloudLIIMS)
MOLECULAR BIOLOGY
- DNA/RNA/protein extraction/purification,
- QPCR, ddPCR, RT-PCR,
- Sequencing (NGS, 16S, WGS, WGBS, Shotgun, and Nanopore)
- DNA/RNA/protein quantification, Nanodrop, Qubit, cDNA preparation, genotyping, library preparation for sequencing
- Microscopy, Western blot, FISH, IHC, ELISA, Luminex
- Terminal restriction fragment length polymorphism (TRFLP), Cloning using PCR and restriction enzymes,
- Deep knowledge/strengths and weaknesses of individual omics technologies
MICROBIOLOGY
- Microbial phenotypic characterization, Aerobic and Anaerobic bacterial culturing using aseptic techniques, Culture media preparation, Optimization of media and fermentation conditions, Working with anaerobic workstations, Gram staining, Colony morphology, Cell morphology, Microbial assay of antibiotics, Microscopy, MALDI-TOF, Flow cytometry
- FACS and biochemical ID (i.e., Vitek-MS), Lyophilization and freeze-drying of bacteria, Live/dead screening using bacterial viability kit, Bacterial counting and enumeration, Bacterial endotoxin measurements using LAL assay, Viable titer (CFU), Bioactivity assays, ELISA, SDS-PAGE, Western blot, HPLC, Bioburden, Cross-immunity assays, Spectrum of Inhibition, Bacteriocin in silico Identification, Transformation and transfection assays, Serological testing, fluorescent in‐situ hybridization
CERTIFICATIONS
1. Whole genome sequencing of bacterial genomes - tools and applications
https://coursera.org/share/bc204c6ba2d4ea856c39a1e7ed254ee4
2. Genomic Data Science: Algorithms for DNA Sequencing
https://coursera.org/share/556d7045d9e7f1fe6b7d2c65916dae60
3. Data Science: Getting and Cleaning Data
https://coursera.org/share/0ec2dfabb572eab3d0f29537ae6d70bd
4. Data Science: R Programming
https://coursera.org/share/691973eeb8ccde8a76efbbd93c8e4ae9
Data Science: Advanced R Programming/Johns Hopkins University
https://coursera.org/share/0ec2dfabb572eab3d0f29537ae6d70bd
Databases and SQL for Data Science/IBM/
https://coursera.org/share/092054dbda6ef79818547536120982d5