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CB204V Single-cell and spatial transcriptomics data analysis 2.5 credits

The course focuses on bioinformatics aspects for single-cell and spatial transcriptomics analysis

Choose semester and course offering

Choose semester and course offering to see current information and more about the course, such as course syllabus, study period, and application information.


For course offering

Autumn 2024 Start 28 Oct 2024 single courses students

Application code


Headings with content from the Course syllabus CB204V (Autumn 2024–) are denoted with an asterisk ( )

Content and learning outcomes

Course contents

The course consists of lectures and computer lab. The lectures focus on theoretical aspects of single-cell and spatial transcriptomic analysis. Computer lab focuses on practical aspects of both subjects. Specific content of the lectures:

  • reproducibility of data analysis
  • Single-cell analysis workflow
  • spatial transcriptomic analysis workflow

Intended learning outcomes

After passing the course, the student should be able to:

  • assess differences between a single-cell and spatial transcriptomic analysis
  • discuss the advantages and disadvantages of both types of analyzes
  • perform a general analysis workflow of single-cell and spatial transcriptomic data

Literature and preparations

Specific prerequisites

A total of 20 university credits (hp) in cell biology, biochemistry, microbiology, gene technology or molecular biology. 6 university credits (hp) in mathematics. English B/6.

Recommended prerequisites

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Examination and completion

If the course is discontinued, students may request to be examined during the following two academic years.

Grading scale

P, F


  • LAB1 - Working in R, 0.5 credits, grading scale: P, F
  • LAB2 - Single-cell analysis, 1.0 credits, grading scale: P, F
  • LAB3 - Spatial Transcriptomics analysis, 1.0 credits, grading scale: P, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Opportunity to complete the requirements via supplementary examination

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Opportunity to raise an approved grade via renewed examination

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Ethical approach

  • All members of a group are responsible for the group's work.
  • In any assessment, every student shall honestly disclose any help received and sources used.
  • In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Further information

Course room in Canvas

Registered students find further information about the implementation of the course in the course room in Canvas. A link to the course room can be found under the tab Studies in the Personal menu at the start of the course.

Offered by

Main field of study


Education cycle

Second cycle

Add-on studies

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