Hello,
I'm relatively new to the field.
Please can someone suggest a list of publicly available datasets for practising genomic data analysis using Rstudio?
Thank you,
Himan
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himanshu0102 •
If you just want something quick to look at, you can download the curated sample study for bell pepper from Verdanta.tech here for free and without registration. It contains precomputed expression data in CSV and Parquet formats, along with an annotation YAML file.
The portal itself currently contains about 60 curated studies, but access to these requires registration.
Bioconductor has a ton of tutorials, workshops and detailed package tutorials.
https://bioconductor.org/help/
Unfortunately your question is too vague to answer properly as 'genomics' is a generic catch all term these days .
Sorry, i mean datasets like on GTEX from where one can download datasets and run an analysis on Rstudio. Are there more resources like GTEX? Thank you.
Cancer genome atlas: https://portal.gdc.cancer.gov/ A different view of the same data at https://www.cbioportal.org/
Allen Brain atlas: https://brain-map.org/our-research/cell-types-taxonomies/cell-types-database-rna-seq-data
ARCHS4 public mining of RNAseq datasets: https://archs4.org/
Expression Atlas: https://www.ebi.ac.uk/gxa/home
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Here’s a nice intro to R (including the use of RStudio) in the context genomics/bioinformatics: https://github.com/hbctraining/Intro-to-R-flipped