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Tufts TTS Research Technology Tutorials - Beta

2023

Tufts TTS Research Technology Tutorials - Beta

About
About
- Introduction
- News
  News
  - 2023 2023
    Table of contents
    
    January 2023
  - 2022
HPC User Guide
HPC User Guide
- Introduction To The Cluster
  Introduction To The Cluster
- Cluster Resources
  Cluster Resources
- Introduction To SLURM
  Introduction To SLURM
- HPC Services
  HPC Services
  - HPC Services
HPC Software/Tools
HPC Software/Tools
- Available HPC Tools
- Python
  Python
- R
  R
- Misc
  Misc
Unix/R/Python Tutorials
Unix/R/Python Tutorials
- Introduction
- Unix
  Unix
  - Intro To Unix
    Intro To Unix
    
    Intro To Linux
    
    Starting with Shell
    
    Bash Parameters
    
    Shell Navigation
    
    Creating & Manipulating Files
    
    Going Home
    
    Running an Interactive Session
    
    Example with BLAST
    
    BLAST Batch Script
- R
  R
  - Intro To R
    Intro To R
    
    Introduction To R OnDemand
    
    R Basics
    
    Data Structures
    
    Functions & Flow
    
    Inspecting/Manipulating Data
    
    Visualization
- Python
  Python
  - Intro To Python
    Intro To Python
    
    Introduction To Python OnDemand
    
    Variables & Data Types
    
    Libraries & Data Frames
    
    Plotting with Plotly
    
    Lists
    
    Loops & Conditionals
    
    Functions & Scope
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

2023

January 2023

TBD