
OmicsLogic Transcriptomics Training Program
The OmicsLogic Transcriptomics program will introduce real-world applications of RNA-seq and provide participants with hands-on skills and logical background to the full RNA-seq analysis approach. We will review methods of quantitative and qualitative analysis of mRNA expression in a sample. Other session will focus on how data is generated using Next Generation Sequencing. Practical sessions will guide participants to use the methods we review on several project datasets to practice generating a table of expression from raw FASTq files and perform subsequent analysis of this table of gene and isoform expression.
Upcoming Events
-
14January
Session 1 – Introduction
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),...
-
17January
Processing of Gene expression NGS data
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,...
-
21January
Differential Gene Expression
Quantification and Generating a table of expression: RSEM, HTSeq, and Sailfish Case study & Hands-on using Cell line project Case study & Hands-on using...
-
24January
Exploratory Data Analysis
Filtering, removing noise and Normalization Techniques Correlation – detecting correlation of features and factors Regression, factors, and features – Factor Regression Analysis overview
-
28January
Analysis of Gene Expression
Unsupervised machine learning (PCA, H-Clust, K-means) Clustering of samples using gene expression profiles Clustering of genes by expression profiles across samples
-
31January
Data Mining using the Multi-Dimensional Expression Data
Supervised Machine learning techniques Factor Regression Analysis, Decision Trees, Random Forest Challenges associated with different kinds of machine learning
-
04February
Machine Learning for Expression Data
Discriminant Analysis and Support Vector Machines Feature Selection and expanding the list of features Data Visualization
-
07February
Interpretation
Annotation using Gene Ontology Human GAGE: Gene Set Enrichment Analysis Statistical Significance and Reproducibility
-
11February
Single-Cell Transcriptomics
Single-cell transcriptomics (SCT) Introduction to SCT, History of SCT, NGS Techniques, Capture techniques, Quantification, scRNA-seq data preparation & Counts
-
13February
ScRNA Transcriptomics Data Analysis
ScRNA data analysis, Publication & projects: Drop-seq data from Ye et al., 2017, Results & Interpretation.
-
14February
Independent project work
Planning your project, 2 Q&A sessions, 1 Presentation Case Studies & Publications Datasets
-
14March
-
Amanda Russell finished the pipeline edgeR Diff 2020-4-1 on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell started the pipeline edgeR Diff 2020-4-1 on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell finished the pipeline Heatmap Utilities 2020-4-1 on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell started the pipeline Heatmap Utilities 2020-4-1 on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell finished the pipeline Heatmap Utilities 2020-4-1 on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell started the pipeline Heatmap Utilities 2020-4-1 on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell finished the pipeline dr heatmap on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell started the pipeline dr heatmap on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell finished the pipeline dr pca on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell started the pipeline dr pca on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell finished the pipeline dr heatmap on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell started the pipeline dr heatmap on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell finished the pipeline DESeq2 Diff 2020-3-30 on server.t-bio.info 9 months, 3 weeks ago
-
Amanda Russell started the pipeline DESeq2 Diff 2020-3-30 on server.t-bio.info 9 months, 3 weeks ago
- Load More
Hello, Amanda, I noticed you are running a heat map visualization on your gene expression data. It is probably going to be too many genes to visualize. I suggest reducing the number of genes to some meaningful number – for example selecting only differentially expressed or something like that.
Thank you, I figured it out!