January 14, 2020

Introduction to the Program

9:30 AM - 10:30 AM

Session Topics: Overview of the entire course, Overview of the tools and resources for this program (edu.t-bio.info courses, projects and datasets, and the T-BioInfo Analytics Platform), Expectations and schedule review for the training program, important deadlines

Introduction to Bioinformatics

Introduction to Bioinformatics

Introduction to big data bioinformatics and its uses in basic research
January 17, 2020

Processing of Gene expression NGS data

9:30 AM - 10:30 AM

Session Topics:

  • Role of pre-processing in standard RNA-seq pipelines (Trimmomatic and PCR-clean)
  • Mapping techniques: mapping on the transcriptome, mapping on the genome and combined strategies (Bowtie, BWA, and TopHat/HiSat)
  • Quantification and Generating a table of expression: RSEM
Transcriptomics 1

Transcriptomics 1

From raw reads to an expression table – basics of processing NGS data Monthly evaluation and discussion of issues
January 21, 2020

Differential Gene Expression

9:30 AM - 10:30 AM

Session Topics:

  • Quantification and Generating a table of expression: RSEM, HTSeq, and Sailfish
  • Case study & Hands-on using Cell line project
  • Case study & Hands-on using Angelman Project
Transcriptomics 2

Transcriptomics 2

Dealing with RNA-seq data – differential gene expression and beyond. Part - 1
January 24, 2020

Exploratory Data Analysis

9:30 AM - 10:30 AM

Session Topics:

  • Filtering, removing noise and Normalization Techniques
  • Correlation – detecting correlation of features and factors
  • Regression, factors, and features – Factor Regression Analysis overview
Transcriptomics 2

Transcriptomics 2

Dealing with RNA-seq data – differential gene expression and beyond. Part - 2
January 28, 2020

Analysis of Gene Expression

9:30 AM - 10:30 AM

Session Topics:

  • Unsupervised machine learning (PCA, H-Clust, K-means)
  • Clustering of samples using gene expression profiles
  • Clustering of genes by expression profiles across samples
Transcriptomics 3

Transcriptomics 3

Introduction to Machine Learning for Transcriptomics data. Part - 1
January 31, 2020

Data Mining using the Multi-Dimensional Expression Data

November 15, 2019 - December 09, 2019 ( All Day )

Session Topics:

  • Supervised Machine learning techniques
  • Factor Regression Analysis, Decision Trees, Random Forest
  • Challenges associated with different kinds of machine learning
Transcriptomics 3

Transcriptomics 3

Introduction to Machine Learning for Transcriptomics data. Part - 2
February 04, 2020

Using Machine Learning for Expression Data

9:30 AM - 10:30 AM

Session Topics:

  • Discriminant Analysis and Support Vector Machines
  • Feature Selection and expanding the list of features
  • Data Visualization
February 07, 2020

Interpretation

9:30 AM - 10:30 AM

Session Topics:

  • Annotation using Gene Ontology
  • Human GAGE: Gene Set Enrichment Analysis
  • Statistical Significance and Reproducibility
February 11, 2020

Single-Cell Transcriptomics

9:30 AM - 10:30 AM

Session Topics: Single-cell transcriptomics (SCT) Introduction to SCT, History of SCT, NGS Techniques, Capture techniques, Quantification, scRNA-seq data preparation & Counts

Transcriptomics 4

Transcriptomics 4

Techniques used to prepare scRNA-seq data. Part - 1
February 13, 2020

ScRNA Transcriptomics Data Analysis

9:30 AM - 10:30 AM

Session Topics: ScRNA data analysis, Publication & projects: Drop-seq data from Ye et al., 2017, Results & Interpretation.

Transcriptomics 4

Transcriptomics 4

Techniques used to prepare scRNA-seq data. Part - 2
February 14, 2020

Independent project work

9:30 AM - 10:30 AM

Session Topics: Planning your project, 2 Q&A sessions, 1 Presentation

  • Case Studies & Publications
  • Datasets
March 14, 2020

Completion of the Program

The end of the program

More Information About the OmicsLogic Transcriptomics Program Curriculum:

To learn more or get help on the curriculum, time requirements, and other questions, please contact us: marketing@pine.bio

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Transcriptomics 2
Transcriptomics 1

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