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45038-01 - Lecture with practical courses: Analysis of Genomics Data with R/Bioconductor (2 CP)
| Semester | spring semester 2022 |
| Course frequency | Every spring sem. |
| Lecturers |
Florian Geier (florian.geier@unibas.ch)
Robert Ivanek (robert.ivanek@unibas.ch, Assessor) Panagiotis Papasaikas (panagiotis.papasaikas@unibas.ch) Julien Roux (julien.roux@unibas.ch) Jenny Charlotte Soneson (jennycharlotte.soneson@unibas.ch) Michael Stadler (michael.stadler@unibas.ch) |
| Content | The R/Bioconductor framework is the most widely used analysis tool for sequence-based bioinformatics. The lecture gives an overview of typical Bioconductor based analysis pipelines including: − NGS data processing (RNAseq, single-cell RNAseq, ATACseq, ChIPseq), with focus on differential expression analysis. − Working with sequence and annotation packages − Programmatic access to public databases − Visualization of genomic data Each lecture is organized around one analysis question using publicly available data. It consists of 1-hour lecture and 1 hour hands on practical. Participants should bring along their laptops. Basic R knowledge is of an advantage. |
| Comments | Each session consists of 1 hour lecture and 1 hour computer exercise. Participants should bring along their laptops. |
| Weblink | Graduate Teaching Program |
| Admission requirements | Maximal number of participants: 40. Prerequisite: Successful participation in the course “Introduction to R (48662-01)” or comparable knowledge of R. Those who are not registered in MOnA (i.e. PostDocs) please send an email to robert.ivanek@unibas.ch directly to apply for the course. |
| Language of instruction | English |
| Use of digital media | No specific media used |
| Interval | Weekday | Time | Room |
|---|---|---|---|
| wöchentlich | Wednesday | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
Dates
| Date | Time | Room |
|---|---|---|
| Wednesday 23.02.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 02.03.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 09.03.2022 | 14.15-16.00 | Fasnachtsferien |
| Wednesday 16.03.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 23.03.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 30.03.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 06.04.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 13.04.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 20.04.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 27.04.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 04.05.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 11.05.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 18.05.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 25.05.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Wednesday 01.06.2022 | 14.15-16.00 | Biozentrum, Seminarraum U1.191 |
| Modules |
Cycle E: Computational and Systems Biology (Master's Studies: Molecular Biology) Doctorate Biochemistry: Recommendations (PhD subject: Biochemistry) Doctorate Biophysics: Recommendations (PhD subject: Biophysics) Doctorate Cell Biology: Recommendations (PhD subject: Cell Biology) Doctorate Computational Biology: Recommendations (PhD subject: Computational Biology) Doctorate Genetics: Recommendations (PhD subject: Genetics) Doctorate Microbiology: Recommendations (PhD subject: Microbiology) Doctorate Molecular Biology: Recommendations (PhD subject: Molecular Biology) Doctorate Neurobiology: Recommendations (PhD subject: Neurobiology) Doctorate Pharmacology: Recommendations (PhD subject: Pharmacology) Doctorate Structural Biology: Recommendations (PhD subject: Structural Biology) |
| Assessment format | continuous assessment |
| Assessment details | There are two grades, in the middle and at the end of the lecture series. No retest. It is required to achieve at least 50% of points overall in order to get the credit points. |
| Assessment registration/deregistration | Reg.: course registration, dereg: cancel course registration |
| Repeat examination | no repeat examination |
| Scale | Pass / Fail |
| Repeated registration | as often as necessary |
| Responsible faculty | Faculty of Science, studiendekanat-philnat@unibas.ch |
| Offered by | Departement Biozentrum |