Omics Logic - Omicslogic Transcriptomics

OmicsLogic Transcriptomics Data Analysis for Biomedical Data is an online mentor-guided program on next-generation sequencing (NGS) data analysis in application to gene expression data with project examples from infectious diseases, cancer & neuroscience. This program will introduce students to real-world applications of RNA-seq Data Analysis in biomedical research and provide hands-on skills and logical background to extract insights from gene expression data.

First, we will review methods and the history of quantitative and qualitative analysis of mRNA expression. Practical sessions will guide participants to use the methods we reviewed on several project datasets to practice generating a table of expression from raw fastq files. This is followed by downstream analysis using simple statistical comparison (t-test), complex statistical comparison (DESEQ2), and advanced statistical methods (unsupervised & supervised machine learning) to derive and interpret important biological insights.

The mentor-guided training & research program will be conducted through Online coursework, video tutorials, and session recordings on OmicsLogic Learn Portal and scheduled live sessions via Zoom. For the analysis of transcriptomics data, students will also have access to the T-BioInfo Platform which combines statistical analysis modules into bioinformatics pipelines. To practice R and Python for data analysis, students will receive access to OmicsLogic Code Playground. At the end of the program completion, students have the opportunity to continue their learning journey in transcriptomics through advanced coursework, example projects, and even an opportunity to carry out an independent bioinformatics research project with the possibility to publish.

To learn more, we welcome you to watch the videos below by our expert mentors and register for a free orientation session:

Transcriptomics Project Examples:

Quantitative and qualitative analysis of RNA

Data preparation using Next Generation Sequencing and preparation of a table of expression from raw FASTq files. Visualization of high-dimensional data using Principal Component Analysis (PCA).

○ Mapping raw reads to reference genome and transcriptome
○ Detecting junctions and assembly of isoforms
○ Quantification of mRNA: Gene, isoform and exon expression table

Advanced analytical approaches

We will look at t-test, then use DESeq2 to run a differential gene expression pipeline and then use Factor Regression Analysis. As a result, you will learn to detect obvious differences between pre-set groups as well as expand that idea to more subtle differences represented by factors that might interact with each other.

○ DIfferential gene and isoform expression
○ Hypothesis testing, p-values, and normalization
○ Multivariate analysis using regressio

Data Exploration and Classification

Supervising and Unsupervised analysis using an example from precision medicine, the methods will be demonstrated to work together to understand cancer subtypes and the use of this information to determine how a new sample can be classified.

○ Data exploration using dimensionality reduction and clustering
○ Classification and discriminant analysis for labeled datasets
○ Cancer subtypes based on gene expression (breast cancer classification)

Single Cell Transcriptomics

scRNA-seq has been demonstrated as a powerful technique for classification of tissue-specific cells and the study of time-course data for thousands of single-cell samples. Data preparation techniques and sparse properties of such data require a new set of methods for its analysis

○ Techniques and protocols for scRNA-seq data preparation
○ Major analytical steps for processing raw single cell sequencing data
○ Analytical techniques to visualize and cluster scRNA-seq data

What's Included?

Choose a program membership type that supports your needs and join a community of our program experts!

45 Days

✅ Online Tutorials

✅ Project Examples

✅ Coding Sessions

✅ Session Recordings

✅ Omicslogic Program Access

✅ Example Demo Cloud Pipelines

✅Online Mentor Support

OUTCOME:

⭐️ Certificate of Completion

⭐️ Case Studies

60 Days

✅ Asynchronous Courses

✅ Project Examples

✅ Group Sessions

✅ One-on-One Mentor Sessions

✅ Omicslogic Program Access

✅ Education Cloud Pipelines

OUTCOME:

⭐️ Literature Review

⭐️ Certificate of Completion

⭐️ Research Poster

90 Days

✅ Asynchronous Courses

✅Project Examples

✅ Group Sessions

✅ One-on-One Mentor Session

✅ Omicslogic Program Access

✅ Education Cloud Pipelines

OUTCOME:

⭐️ Certificate of Excellence

⭐️ Project Report

⭐️ Research Paper Publication

Program Syllabus : Transcriptomics

SESSIONS TITLE	DESCRIPTION
	Introduction to NGS Transcriptomics mRNA Biology Methods of RNA quantification mRNA library preparation Next-generation Sequencing Illumina, Microarray, Oxford Nanopore, PacBio
	Processing Transcriptomics Data Read quality: FastQC Pre-processing: Trimmomatic and PCR Clean Strategies for mapping Exon and Junction detection Quantification strategie
	Precision Medicine Projects Projects: Literature Review and Publication Modeling Precision Medicine in Breast cancer Cell Lines and High Throughput Drug Testing Cancer Classification Targeted Treatment
	Loading RNA-Seq data in R and Python Loading CSV, Excel or TXT files. Determine numeric and non-numeric data types. Preparing a matrix and a data frame. Creating variables and functions
	Normalization and Preparation for Analysis Statistical Properties of Data Quantification strategies Removing NA and Zero values Log scale transformation
	Data Visualization in R and Python Computation of summary statistics Boxplots, Scatterplots, and Bar Plots Density Plots, Histograms, and Heatmaps Data transformation and Scaling
	Exploratory Analysis Descriptive statistics Finding outliers Variance and Interpretation Adjusting scaling and normalization Removing low value data Addressing common issues
	Differential Gene Expression T-test and statistical considerations p-value and Fold change FDR and Benjamini Adjustment DESEQ2 and EDGER Volcano and MA Plots Heat map for selected genes
	Regression Analysis Variance and factors, ANOVA Factor levels and preparation for analysis Regression and Factor Regression Analysis Interpretation of results
	Biological Interpretation DAVID and ENRICHr Gene Set Enrichment Analysis (GSEA) KEGG pathways annotation Gene Ontology (GO) Biological Processes Molecular function and Cellular Components
	Single Cell RNA-Seq methods and analysis approaches for cell type decomposition Single-cell transcriptomics (SCT) Introduction to SCT, History of SCT, NGS Techniques, Capture techniques, Quantification, scRNA-seq data preparation & Counts ScRNA data analysis, Publication & projects: Drop-seq data from Ye et al., 2017, Results & Interpretation.
	Case Studies Examples from oncology, neuroscience science and infectious diseases Components of bioinformatics analysis Literature review, compiling a primary dataset, developing an analysis plan, performing exploratory analysis, data processing and preparation, statistical analysis, biological interpretation and validation


Learn how to analyze RNA-Seq data on the T-BioInfo platform	Understand methods and approaches for RNA-seq	Start running R code for visualization and analysis	Learn Python code for visualization and analysis	Explore Project Case Studies in various topics

Transcriptomics Project Examples:

45 Days

✅ Online Tutorials

✅ Project Examples

✅ Coding Sessions

✅ Session Recordings

✅ Omicslogic Program Access

✅ Example Demo Cloud Pipelines

✅Online Mentor Support

60 Days

✅ Asynchronous Courses

✅ Project Examples

✅ Group Sessions

✅ One-on-One Mentor Sessions

✅ Omicslogic Program Access

✅ Education Cloud Pipelines

90 Days

✅ Asynchronous Courses

✅Project Examples

✅ Group Sessions

✅ One-on-One Mentor Session

✅ Omicslogic Program Access

✅ Education Cloud Pipelines

Program Syllabus : Transcriptomics

Example Projects & Research Projects by OmicsLogic Research Fellows

Register for the Upcoming Webinar Session:

Resources and Training Session Examples

LINKS

Subscribe to our Newsletter