nih finding data

Short slides on genomic data for the NIH data science (DS) bootcamp 2021-07-12 organized by Allissa Dillman.

Transcript

1. NIH DS bootcamp: finding data panel Leonardo Collado Torres lcolladotor.github.io 2021-07-12
2. LIEBER INSTITUTE for BRAIN DEVELOPMENT https://en.wikipedia.org/wiki/FASTQ_format Genomics raw data: FASTQ files
3. LIEBER INSTITUTE for BRAIN DEVELOPMENT https://www.ncbi.nlm.nih.gov/sra
4. LIEBER INSTITUTE for BRAIN DEVELOPMENT https://pubmed.ncbi.nlm.nih.gov/29379135/
5. LIEBER INSTITUTE for BRAIN DEVELOPMENT https://www.nature.com/articles/543007a
6. https://jhubiostatistics.shinyapps.io/recount/
7. LIEBER INSTITUTE for BRAIN DEVELOPMENT http://rna.recount.bio/
8. 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
9. 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
10. LIEBER INSTITUTE for BRAIN DEVELOPMENT http://bioconductor.org/packages/ExperimentHub/
11. LIEBER INSTITUTE for BRAIN DEVELOPMENT