Dates: 6-7 June, 2019
Venue: Auditorium 4th floor Fundacion Ciencia & Vida. Av. Zañartu 1482, Ñuñoa
The objective of the course is to become familiar with fundamentals of data analysis in R, through the use of publically available RNAseq/clinical data, so that attendees can go and do analyses to answer cancer and/or immunology questions with RNAseq data.
Eligibility: Postdocs and PhD students with background in cancer, immunology and/or genetics.
This course is limited to 30 attendees. Fee: $25.000
Please submit a letter of intent and CV to lladserlab@cienciavida.org
Outline:
Thursday 6th of June – Morning (9am to 12:30pm)
An introduction to R:
– Concept of programming language
– Rstudio environment
– Types of data
– Installing packages
– Getting data into the environment
Manipulating/reshaping data to make it suitable for plotting/analysis:
Common tasks (filtering, duplicating, merging, grouping, …) using gene signatures as an example
Thursday 6th of June – Afternoon (1:30pm to 5pm)
Specific plotting of interest:
– ggplot (scatter, boxplot, …)
– Heatmaps
– Dimension reduction (PCA, tSNE, UMAP)
– Exporting plots
Specific analyses of interest:
– Common statistical tests (correlations, t-test, …)
– Survival analysis
Friday 7th of June – Morning (9am to 12:30pm)
Problem solving by groups of 3:
– Find a gene signature in the literature
– Find/import relevant TCGA data
– Calculate enrichment values
– Correlation with a list of genes
– Survival analysis on the enrichment scores
– Plot survival curves and enrichment scores distribution
Teachers:
Ehsan Ghorani, PhD, University College London Marc Robert de Massy, University College London
Organizers:
Alvaro Lladser, PhD, Fundación Ciencia & Vida
Fabiola Osorio, PhD, ICBM, Faculty of Medicine, Universidad de Chile Fundación Ciencia & VIda
Asociación Chilena de Inmunología – ASOCHIN
Funding:
Basal AFB 170004
FONDECYT (1171703, 1161212)
HHMI International Research Scholar Grant
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