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Tufts TTS Research Technology Tutorials - Beta

Model Performance

Tufts TTS Research Technology Tutorials - Beta

About
About
- Introduction
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  - 2022
HPC User Guide
HPC User Guide
- Introduction To The Cluster
  Introduction To The Cluster
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Unix/R/Python Tutorials
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    Intro To Linux
    
    Starting with Shell
    
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    Going Home
    
    Running an Interactive Session
    
    Example with BLAST
    
    BLAST Batch Script
- R
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  - Intro To R
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- Python
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  - Intro To Python
    Intro To Python
    
    Introduction To Python OnDemand
    
    Variables & Data Types
    
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    Lists
    
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Omics Tutorials
Omics Tutorials
- Introduction
- Genomics
  Genomics
  - NGS Tips & Tricks
    NGS Tips & Tricks
    
    Fastq Manipulation
  - Intro To NGS
    Intro To NGS
    
    Background
    
    Setup
    
    Quality Control
    
    Alignment
    
    Alignment Cleanup
    
    Variant Calling
    
    Variant Annotation
  - Intro To 16S Metabarcoding
    Intro To 16S Metabarcoding
    
    Background
    
    Setup
    
    Quality Control
    
    Error Model & ASVs
    
    Merging, Chimeras & Taxonomy
    
    Diversity Analysis
    
    Differential Abundance
- Transcriptomics
  Transcriptomics
  - Intro To RNA-Seq
    Intro To RNA-Seq
    
    Background
    
    Setup
    
    Quality Control
    
    Read Alignment
    
    Gene Quantification
    
    Differential Expression
    
    Pathway Enrichment
- Proteomics
  Proteomics
  - Intro To Proteomics
    Intro To Proteomics
    
    Background
    
    Setup
  - Intro To AlphaFold2
    Intro To AlphaFold2
    
    Background
    
    Setup
    
    AlphaFold2 Pre-Processing
    
    AlphaFold2 Evoformer/Structure Module
    
    AlphaFold2 Output
    
    PyMOL Visualization
    
    Optional: AlphaFold2 Batch Script
Biostatistics
Biostatistics
- Introduction To Biostatistics
- Setup
- Variables and Sampling
  Variables and Sampling
- Analyzing One Categorial Variable
  Analyzing One Categorial Variable
  - Binomial Test
- Analyzing Two Categorical Variables
  Analyzing Two Categorical Variables
- Analyzing One Numeric Variable
  Analyzing One Numeric Variable
  - One Sample T-Test
- Analyzing Numeric Variable With Two Groups
  Analyzing Numeric Variable With Two Groups
  - Paired T-Test
  - Two Sample T-Test
- Analyzing Two Numeric Variables
  Analyzing Two Numeric Variables
  - Correlation
- Analyzing Two Or More Groups
  Analyzing Two Or More Groups
  - One-Way ANOVA
Machine Learning
Machine Learning
- Introduction To Machine Learning
  Introduction To Machine Learning
  - Introduction To Machine Learning
  - Tutorial Setup
- Unsupervised Learning
  Unsupervised Learning
- Supervised Learning
  Supervised Learning
  - Linear Models
  - Logistic Regression
  - Survival Analysis Part 1
  - Survival Analysis Part 2
  - Multivariate Regression
  - Model Performance Model Performance
    Table of contents
    
    Training and Testing Data
    
    Model Error
    
    Sensitivity v. Specificity
    
    Area Under The Curve
    
    References

Introduction To Model Performance

Prerequisites

Request an account on the Tufts HPC Cluster
Connect to the VPN
Please be sure to have followed the instructions on the setup page

Training and Testing Data

Model Error

Sensitivity v. Specificity

Area Under The Curve

References