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NIH DS bootcamp:
finding data panel
Leonardo Collado Torres
lcolladotor.github.io
2021-07-12
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LIEBER INSTITUTE for BRAIN DEVELOPMENT
https://en.wikipedia.org/wiki/FASTQ_format
Genomics raw data: FASTQ files
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LIEBER INSTITUTE for BRAIN DEVELOPMENT
https://www.ncbi.nlm.nih.gov/sra
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LIEBER INSTITUTE for BRAIN DEVELOPMENT
https://pubmed.ncbi.nlm.nih.gov/29379135/
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LIEBER INSTITUTE for BRAIN DEVELOPMENT
https://www.nature.com/articles/543007a
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https://jhubiostatistics.shinyapps.io/recount/
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LIEBER INSTITUTE for BRAIN DEVELOPMENT
http://rna.recount.bio/
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expression data for ~70,000 human samples
samples
phenotypes
?
GTEx
N=9,962
TCGA
N=11,284
SRA
N=49,848
samples
expression
estimates
gene
exon
junctions
ERs
Answer meaningful
questions about
human biology and
expression
slide adapted from Shannon Ellis
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Category Frequency
F 95
female 2036
Female 51
M 77
male 1240
Male 141
Total 3640
Even when information is provided, it’s not always clear…
sra_meta$Sex
“1 Male, 2 Female”, “2 Male, 1 Female”, “3
Female”, “DK”, “male and female” “Male (note:
….)”, “missing”, “mixed”, “mixture”, “N/A”, “Not
available”, “not applicable”, “not collected”,
“not determined”, “pooled male and female”,
“U”, “unknown”, “Unknown”
slide adapted from Shannon Ellis
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LIEBER INSTITUTE for BRAIN DEVELOPMENT
http://bioconductor.org/packages/ExperimentHub/
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LIEBER INSTITUTE for BRAIN DEVELOPMENT