Host professor's lecture - MB151P120

• Title: Host professor's lecture
• Czech title: Přednášky hostujících profesorů
• Guaranteed by: Department of Cell Biology (31-151)
• Faculty: Faculty of Science
• Actual: from 2019
• Semester: both
• E-Credits: 3
• Hours per week, examination: 2/0, Ex [HT]
• Capacity: 25
• Min. number of students: unlimited
• 4EU+: no
• Virtual mobility / capacity: no
• State of the course: taught
• Language: English
• Note: you can enroll for the course repeatedly; enabled for web enrollment; you can enroll for the course in winter and in summer semester
• Guarantor: prof. RNDr. Jan Černý, Ph.D.
• Teacher(s): prof. RNDr. Jan Černý, Ph.D.

Annotation

English

Basic computer skills for processing, visualizing, and interpreting single-cell RNA-seq (scRNA-seq) data. Basic R programming will be introduced. Publicly available scRNA-seq data from current biology research will be used to illustrate the steps involved in the analysis.

Last update: Šebková Nataša, RNDr., Ph.D. (24.10.2019)

Czech

Základní počítačové dovednosti pro zpracování, vizualizaci a interpretaci jednobuněčných dat RNA-seq (scRNA-seq). Bude představeno základní programování R. Pro ilustraci kroků zapojených do analýzy budou použity veřejně dostupné údaje o scRNA-seq z aktuálního biologického výzkumu.

Last update: Šebková Nataša, RNDr., Ph.D. (24.10.2019)

Literature

English

Martin Hemberg et al. Analysis of Single-Cell RNA-Seq Data.

(PDF file will be distributed for free.)

Last update: Šebková Nataša, RNDr., Ph.D. (24.10.2019)

Requirements to the exam

English

Project assignments           80%

Final project presentation 20%

 

Last update: Šebková Nataša, RNDr., Ph.D. (24.10.2019)

Czech

Zadání projektu 80%
Závěrečná prezentace projektu 20%

Last update: Šebková Nataša, RNDr., Ph.D. (24.10.2019)

Syllabus

English

Single-cell RNA-seq data analysis

Summer 2019

Charles University

 

Course Description:

Basic computer skills for processing, visualizing, and interpreting single-cell RNA-seq (scRNA-seq) data. Basic R programming will be introduced. Publicly available scRNA-seq data from current biology research will be used to illustrate the steps involved in the analysis.

 

Instructor:

Joe Song ([e-mail])

Fulbright Visiting Professor, Department of Cell Biology, Charles University

Professor of Computer Science, Faculty Member of Molecular Biology
New Mexico State University

 

Prerequisite:

1.    Basics of molecular biology.

2.    Some exposure to programming languages such as R, SAS, Python, C/C++, or MATLAB are highly desirable. However, the course will introduce the basics of R programming.

 

Meeting time:

            Mondays 14:50—16:20 from 18/02/2019 to 17/05/2019 (13 weeks)

Examination period 27/05/2019 to 30/06/2019

 

Projects:

Select a scRNA-seq data set of interest to their own research. Then apply the data analysis methods learned in class on the data set.

 

Grading:

            Project assignments           80%

            Final project presentation 20%

 

Textbook:

Martin Hemberg et al. Analysis of Single-Cell RNA-Seq Data.

(PDF file will be distributed for free.)

 

Topics:

Week 1. Introduction to single cell RNA sequencing

Week 2. Introduction to R and bioconductor

Week 3. Expression data quality control

Week 4. Normalization of library size

Week 5. Removing unwanted confounders

Week 6. Cluster analysis

Week 7. Gene selection

Week 8. Differential expression analysis

Week 9. Trajectory inference

Week 10. Meta-analysis

Week 11. Sequencing reads quality control

Week 12. Mapping scRNA reads to genes

 

 

Last update: Půta František, doc. RNDr., CSc. (05.02.2019)

Czech

Témata:
1. týden Úvod do sekvenování jednotlivých buněk RNA
Týden 2. Úvod do R a bioconductor
Týden 3. Kontrola kvality dat
4. týden Normalizace velikosti knihovny
5. týden Odstranění nežádoucích zmatků
6. týden Clusterová analýza
7. týden Výběr genu
8. týden Analýza diferenciální exprese
Týden 9. Inference trajektorie
10. týden Meta-analýza
11. týden Sekvenování čte kontrolu kvality
12. týden Mapování scRNA čte na geny

Last update: Šebková Nataša, RNDr., Ph.D. (24.10.2019)