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Tufts TTS Research Technology Tutorials - Beta
Introduction
Initializing search
GitHub
About
HPC User Guide
HPC Software/Tools
Unix/R/Python Tutorials
Omics Tutorials
Biostatistics
Machine Learning
Tufts TTS Research Technology Tutorials - Beta
GitHub
About
About
Introduction
News
News
2023
2022
HPC User Guide
HPC User Guide
Introduction To The Cluster
Introduction To The Cluster
What Is The Cluster?
Request an Account
Navigate To The Cluster
File Transfer
Cluster Resources
Cluster Resources
Cluster Storage Request
Cluster Storage Increase Request
Compute Resources
Software On The Cluster
Introduction To SLURM
Introduction To SLURM
Interactive Session
Submitting A Batch Job
Checking Job Status
HPC Services
HPC Services
HPC Services
HPC Software/Tools
HPC Software/Tools
Available HPC Tools
Python
Python
Python Interactive Session
JupyterLab
Conda Environments
R
R
R Interactive Session
R Batch Jobs
RStudio OnDemand
Misc
Misc
GitHub
Rclone
Containers
Nextflow
Parallel
API (Application Programming Interface)
dbGAP Downloads
Tufts VDI
Unix/R/Python Tutorials
Unix/R/Python Tutorials
Introduction
Introduction
Table of contents
Unix Tutorials
R Tutorials
Python Tutorials
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
Quantitative Variables
Qualitative Variables
Sampling
Confidence Intervals
Probability Distributions
Analyzing One Categorial Variable
Analyzing One Categorial Variable
Binomial Test
Analyzing Two Categorical Variables
Analyzing Two Categorical Variables
Odds
Risk/Odds Ratio
Fisher's Exact Test
Chi-Square Test
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
Dimension Reduction
Distance Metrics
K-Means Clustering
Hierarchical Clustering
Supervised Learning
Supervised Learning
Linear Models
Logistic Regression
Survival Analysis Part 1
Survival Analysis Part 2
Multivariate Regression
Model Performance
Table of contents
Unix Tutorials
R Tutorials
Python Tutorials
Introduction
Unix Tutorials
Intro To Unix
R Tutorials
Intro To R
Python Tutorials
Intro To Python