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February 2021

W14: Intro to Modern Statistics with R

February 16 @ 1:30 pm - February 18 @ 3:30 pm
ZOOM CA United States + Google Map

Through this seminar, attendees will walk away knowing when and how to run modern versions of traditional statistical analysis. These tests and the underlying bioinformatical lesson about resampling will be of use to most scientific disciplines. The course makes no assumptions about familiarity with traditional statistics – we will simply go through relatable experimental examples and ask how to test various hypotheses, introducing the relevant methods along the way. There will be homework assignments each night to solidify the concepts…

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W11: Metagenomics Analysis with Python and R

February 16 @ 9:00 am - February 18 @ 12:00 pm
ZOOM CA United States + Google Map

This workshop provides an introduction to the microbiome analyses from the raw sequence data generated from the next-generation sequencing platforms. We will cover how to perform the 16S rRNA-based analysis using an open-source bioinformatics pipeline QIIME. We will also cover some downstream analyses of the microbiome data beyond QIIME, including statistical analyses and functional analyses.

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W3: Intro to R and Data Visualization

February 16 @ 9:00 am - February 18 @ 12:00 pm
ZOOM CA United States + Google Map

R (www.r-project.org) is a free software environment for statistical computing and graphics. First, this workshop introduces basic concepts, syntax, and usage in R programming, statistical analysis, and visualization techniques. We will conduct hands-on tutorials throughout the session, giving attendees a chance to see R in action. This course is a pre-requisite for several other Collaboratory workshops. This workshop is geared towards researchers who have little or no experience with R who want to get started with importing data into R…

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W20: Single-Cell RNA-Seq Analysis with Python

February 9 @ 1:30 pm - February 12 @ 4:30 pm
ZOOM CA United States + Google Map

This workshop aims to introduce the basic concepts and algorithms for single-cell RNA-seq analysis. It will help participants obtain a better idea of how to use scRNA-seq technology, from considerations in experimental design to data analysis and interpretation. This workshop can serve researchers who are interested in designing an scRNA-seq study or who have acquired scRNA-seq data and would like to learn about different analytical approaches.  

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W22: Advanced Cytoscape

February 2 @ 9:00 am - February 4 @ 12:00 pm
ZOOM CA United States + Google Map

The workshop will cover experimental approaches to protein interaction determination; processing and presentation of interaction data available from online resources, and the role of interaction data in the interpretation of large scale datasets.

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January 2021

W16: Library Prep for NGS

January 26 @ 1:30 pm - January 28 @ 4:30 pm
ZOOM CA United States + Google Map

This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq, ChIP-seq, RNA-seq, Methyl-seq) are explained the first and second day in class. The third day, Quality Control steps of the starting input material and final libraries are performed in the Lab (TapeStation). Purification from Primer Dimers (using AMPure beads) and Library Submission is also performed on the same day. The third day is optional, sign-up is required.

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W12: Intro to Matlab

January 19 @ 9:30 am - January 21 @ 12:00 pm
ZOOM CA United States + Google Map

MATLAB is a powerful, high-level programing language for numerical computation, visualization, and application development. This workshop will start by introducing the MATLAB environment and then cover working with arrays and matrices, loops and conditional statements, writing your own functions, working with files and visualizing your data. The final day will briefly introduce utilizing MATLAB to solve differential equations and the basics of computational systems biology modeling using MATLAB. The course is supplemented with many hands-on exercises. The workshop is suitable…

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W18: Advanced Python

January 12 @ 1:30 pm - January 14 @ 4:30 pm
ZOOM CA United States + Google Map

This workshop will cover some more advanced topics in python including an overview of object-oriented python (this will not be an in-depth course on object-oriented programming), use of the numpy and pandas libraries (python libraries for efficient handling of large numeric and heterogenous datasets, and matplotlib for plotting results. At the end of this workshop, students will better understand the python data structures for handling large datasets and will have some knowledge of how to manipulate these data and plot…

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W2: Using NGS Analysis Tools

January 12 @ 9:00 am - January 14 @ 12:00 pm
ZOOM CA United States + Google Map

High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. First, this workshop introduces the more “universal” aspects of high-throughput sequence analysis—from experimental design to sequencing and alignment methods. Next, this workshop covers common file formats for sequence data and limitations of sequencing technologies. We will explore a hands-on exercise using the Hoffman2 cluster and will use programs designed to analyze read data, clean artifact and low-quality sequences, and align short…

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W9: Intro to Python

January 5 @ 1:30 pm - January 7 @ 4:30 pm
ZOOM CA United States + Google Map

This workshop will cover the basic concepts of Python programming. The course is supplemented with many hands-on exercises with emphasis given towards computational biology use cases.

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