Public datatutorialoverview
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This talk reviews some of the software packages available for R and Bioconductor to access NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). In particular, the GEOquery, GEOmetadb, and SRAdb packages are discussed.
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Public datatutorialoverview
- 1. Accessing 油Public 油Data 油 油 (from 油NCBI) 油Using 油Bioconductor 油
- 2. Na#onal 油Ins#tutes 油of 油Health 油
- 3. Objec#ves 油 ≒ Navigate 油NCBI 油GEO 油website 油 ≒ Understand 油NCBI 油GEO 油data 油en<<es 油and 油rela#onships 油 between 油them 油 ≒ Use 油GEOquery 油package 油to 油import 油data 油from 油NCBI 油GEO 油into 油 R 油 ≒ Convert 油GEOquery 油data 油structures 油into 油R 油data 油structures 油 ≒ Use 油GEOmetadb 油to 油鍖nd 油data 油in 油NCBI 油GEO 油 ≒ Know 油rela#onship 油between 油NCBI 油GEO 油and 油NCBI 油SRA 油 ≒ Understand 油how 油to 油use 油the 油SRAdb 油package 油to 油query 油SRA 油 metadata 油 ≒ Use 油SRAdb 油package 油to 油control 油the 油Integrated 油Genome 油 Viewer 油(IGV) 油from 油R 油
- 5. MIAME-足compliant 油Data 油 ≒ The 油raw 油data 油for 油each 油hybridiza#on 油(e.g., 油CEL 油or 油GPR 油鍖les) 油 ≒ The 油鍖nal 油processed 油(normalized) 油data 油for 油the 油set 油of 油hybridiza#ons 油in 油the 油 experiment 油(study) 油(e.g., 油the 油gene 油expression 油data 油matrix 油used 油to 油draw 油the 油 conclusions 油from 油the 油study) 油 ≒ The 油essen#al 油sample 油annota#on 油including 油experimental 油factors 油and 油their 油 values 油(e.g., 油compound 油and 油dose 油in 油a 油dose 油response 油experiment) 油 ≒ The 油experimental 油design 油including 油sample 油data 油rela#onships 油(e.g., 油which 油 raw 油data 油鍖le 油relates 油to 油which 油sample, 油which 油hybridiza#ons 油are 油technical, 油 which 油are 油biological 油replicates) 油 ≒ Su鍖cient 油annota#on 油of 油the 油array 油(e.g., 油gene 油iden#鍖ers, 油genomic 油 coordinates, 油probe 油oligonucleo#de 油sequences 油or 油reference 油commercial 油 array 油catalog 油number) 油 ≒ The 油essen#al 油laboratory 油and 油data 油processing 油protocols 油(e.g., 油what 油 normaliza#on 油method 油has 油been 油used 油to 油obtain 油the 油鍖nal 油processed 油data) 油
- 6. Whats 油in 油GEO 油 ≒ Gene 油expression 油pro鍖ling 油by 油microarray 油or 油next-足genera#on 油 sequencing 油 ≒ Non-足coding 油RNA 油pro鍖ling 油by 油microarray 油or 油next-足genera#on 油 sequencing 油 ≒ Chroma#n 油immunoprecipita#on 油(ChIP) 油pro鍖ling 油by 油 microarray 油or 油next-足genera#on 油sequencing 油 ≒ Genome 油methyla#on 油pro鍖ling 油by 油microarray 油or 油next-足 genera#on 油sequencing 油 ≒ Genome 油varia#on 油pro鍖ling 油by 油array 油(arrayCGH) 油 ≒ SNP 油arrays 油 ≒ Serial 油Analysis 油of 油Gene 油Expression 油(SAGE) 油 ≒ Protein 油arrays 油
- 7. GEO 油data 油en##es 油 ≒ GEO 油Samples 油(GSM) 油 ≒ GEO 油PlaYorm 油(GPL) 油 ≒ GEO 油Series 油(GSE) 油 Collec#ons 油of 油related 油GSM 油and 油GPL 油along 油with 油free-足text 油 study 油metadata 油 Two 油data 油鍖avors 油 ≒ GSE 油 ≒ GSEMatrix 油 ≒ GEO 油Dataset 油(GDS) 油 油 Only 油data 油en#ty 油that 油is 油curated 油by 油NCBI 油GEO 油sta鍖 油 Typically, 油samples 油are 油divided 油into 油sta#s#cally 油and 油 biologically 油relevant 油groups 油upon 油which 油we 油can 油compute 油
- 8. NCBI 油GEO 油website 油 ≒ h^p://www.ncbi.nlm.nih.gov/geo/ 油
- 9. GEO 油SOFT 油Format 油
- 10. GEO 油SOFT 油Format 油
- 11. GEOquery 油 ≒ Singular 油goal: 油Get 油data 油from 油NCBI 油GEO 油and 油 parse 油into 油R 油objects 油 ≒ Secondary 油goals: 油 Get 油supplemental 油鍖les 油from 油NCBI 油GEO 油 Allow 油large-足scale 油data 油mining 油by 油doing 油all-足of-足the-足 above 油in 油a 油lossless 油manner 油
- 12. GEOquery 油Data 油Structures 油 油 (GSM, 油GPL, 油GDS) 油
- 13. GEOquery 油Data 油Structures 油 (GSE) 油
- 14. GEOquery 油Walkthrough 油 ≒ h^p://watson.nci.nih.gov/~sdavis/ 油 Click 油on 油Tutorials 油and 油then 油on 油Accessing 油public 油 data. 油 ≒ Download 油the 油R 油script 油for 油cut-足and-足paste 油to 油 follow 油along 油
- 15. GEOmetadb 油 ≒ Finding 油data 油in 油NCBI 油GEO 油can 油be 油challenging 油 ≒ Some 油inves#gators 油need 油large-足scale, 油 computable 油access 油to 油GEO 油metadata 油 ≒ Given 油one 油GEO 油en#ty 油type, 油it 油may 油be 油useful 油to 油 鍖nd 油all 油rela#onships 油with 油other 油en#ty 油types 油 (eg., 油鍖nd 油all 油hgu133a 油arrays 油in 油GEO) 油
- 16. GEOmetadb 油 ≒ What 油is 油GEOmetadb? 油 油A 油Bioconductor 油package 油that 油o鍖ers 油an 油alterna#ve 油 to 油eU#ls 油data 油mining 油of 油GEO 油metadata 油 A 油SQLite 油database 油which 油stores 油all 油the 油GEO 油 metadata 油in 油a 油rela#onal 油format 油for 油easy 油querying, 油 par#cularly 油in 油bulk 油 ≒ What 油is 油GEOmetadb 油NOT? 油 We 油have 油not 油a^empted 油to 油alter 油or 油standardize 油in 油 any 油way 油the 油data 油from 油GEO 油
- 20. SRAdb 油 ≒ Similar 油goals 油to 油GEOmetadb, 油but 油with 油SRA 油 data 油 ≒ Data 油for 油SRA 油(ENA, 油DRA) 油are 油mirrored, 油but 油 exact 油policies 油are 油a 油bit 油unclear 油(to 油me) 油 ≒ Accessing 油to 油the 油data 油also 油provided 油by 油SRAdb 油 package, 油but 油further 油processing 油(SRA 油SDK) 油 now 油needed 油to 油get 油FASTQ 油鍖les 油
- 21. SRAdb 油and 油NCBI 油SRA 油 Recently, 油NCBI 油announced 油that 油due 油to 油budget 油constraints, 油it 油would 油be 油discon#nuing 油its 油 Sequence 油Read 油Archive 油(SRA) 油and 油Trace 油Archive 油repositories 油for 油high-足throughput 油 sequence 油data. 油However, 油NIH 油has 油since 油commi^ed 油interim 油funding 油for 油SRA 油in 油its 油current 油 form 油un#l 油October 油1, 油2011. 油In 油addi#on, 油NCBI 油has 油been 油working 油with 油sta鍖 油from 油other 油NIH 油 Ins#tutes 油and 油NIH 油grantees 油to 油develop 油an 油approach 油to 油con#nue 油archiving 油a 油widely 油used 油 subset 油of 油next 油genera#on 油sequencing 油data 油ajer 油October 油1, 油2011. 油 We 油now 油plan 油to 油con#nue 油handling 油sequencing 油data 油associated 油with: 油 ≒RNA-足Seq, 油ChIP-足Seq, 油and 油epigenomic 油data 油that 油are 油submi^ed 油to 油GEO 油 ≒Genomic 油and 油Transcriptomic 油assemblies 油that 油are 油submi^ed 油to 油GenBank 油 ≒16S 油ribosomal 油RNA 油data 油associated 油with 油metagenomics 油that 油are 油submi^ed 油to 油GenBank 油 In 油addi#on, 油NCBI 油will 油con#nue 油to 油provide 油access 油to 油exis#ng 油SRA 油and 油Trace 油Archive 油data 油 for 油the 油foreseeable 油future. 油NCBI 油is 油also 油con#nuing 油to 油discuss 油with 油NIH 油Ins#tutes 油 approaches 油for 油handling 油other 油next-足genera#on 油sequencing 油data 油associated 油with 油speci鍖c 油 large-足scale 油studies. 油
- 22. SRAdb 油and 油IGV 油Walkthrough 油 ≒ Download 油and 油start 油IGV: 油 h^p://www.broadins#tute.org/sojware/igv/ download 油