Omic association studies with R and Bioconductor / (Record no. 130516)
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| 000 -LEADER | |
|---|---|
| fixed length control field | 06082cam a2200649Ii 4500 |
| 001 - CONTROL NUMBER | |
| control field | 9780429440557 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | FlBoTFG |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20220509193129.0 |
| 006 - FIXED-LENGTH DATA ELEMENTS--ADDITIONAL MATERIAL CHARACTERISTICS--GENERAL INFORMATION | |
| fixed length control field | m o d |
| 007 - PHYSICAL DESCRIPTION FIXED FIELD--GENERAL INFORMATION | |
| fixed length control field | cr cnu---unuuu |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 190618s2019 flu ob 001 0 eng d |
| 040 ## - CATALOGING SOURCE | |
| Original cataloging agency | OCoLC-P |
| Language of cataloging | eng |
| Description conventions | rda |
| -- | pn |
| Transcribing agency | OCoLC-P |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 9780429803369 |
| -- | (electronic bk.) |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 0429803362 |
| -- | (electronic bk.) |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 9780429440557 |
| -- | (electronic bk.) |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 0429440553 |
| -- | (electronic bk.) |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 9780429803376 |
| -- | (electronic bk. : PDF) |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 0429803370 |
| -- | (electronic bk. : PDF) |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 9780429803352 |
| -- | (electronic bk. : Mobipocket) |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 0429803354 |
| -- | (electronic bk. : Mobipocket) |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| Cancelled/invalid ISBN | 9781138340565 |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| Cancelled/invalid ISBN | 1138340561 |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (OCoLC)1104841012 |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (OCoLC-P)1104841012 |
| 050 #4 - LIBRARY OF CONGRESS CALL NUMBER | |
| Classification number | QH442 |
| Item number | .G6475 2019eb |
| 072 #7 - SUBJECT CATEGORY CODE | |
| Subject category code | SCI |
| Subject category code subdivision | 007000 |
| Source | bisacsh |
| 072 #7 - SUBJECT CATEGORY CODE | |
| Subject category code | MAT |
| Subject category code subdivision | 029000 |
| Source | bisacsh |
| 072 #7 - SUBJECT CATEGORY CODE | |
| Subject category code | SCI |
| Subject category code subdivision | 008000 |
| Source | bisacsh |
| 072 #7 - SUBJECT CATEGORY CODE | |
| Subject category code | PS |
| Source | bicssc |
| 082 04 - DEWEY DECIMAL CLASSIFICATION NUMBER | |
| Classification number | 572/.33 |
| Edition number | 23 |
| 100 1# - MAIN ENTRY--PERSONAL NAME | |
| Personal name | González, Juan R. |
| Titles and other words associated with a name | (Bioinformatics researcher), |
| Relator term | author. |
| 245 10 - TITLE STATEMENT | |
| Title | Omic association studies with R and Bioconductor / |
| Statement of responsibility, etc | Juan R. González, Alejandro Cáceres. |
| 264 #1 - | |
| -- | Boca Raton, Florida : |
| -- | CRC Press, |
| -- | [2019] |
| 264 #4 - | |
| -- | ©2019 |
| 300 ## - PHYSICAL DESCRIPTION | |
| Extent | 1 online resource. |
| 336 ## - | |
| -- | text |
| -- | txt |
| -- | rdacontent |
| 337 ## - | |
| -- | computer |
| -- | c |
| -- | rdamedia |
| 338 ## - | |
| -- | online resource |
| -- | cr |
| -- | rdacarrier |
| 520 ## - SUMMARY, ETC. | |
| Summary, etc | After the great expansion of genome-wide association studies, their scientific methodology and, notably, their data analysis has matured in recent years, and they are a keystone in large epidemiological studies. Newcomers to the field are confronted with a wealth of data, resources and methods. This book presents current methods to perform informative analyses using real and illustrative data with established bioinformatics tools and guides the reader through the use of publicly available data. Includes clear, readable programming codes for readers to reproduce and adapt to their own data. Emphasises extracting biologically meaningful associations between traits of interest and genomic, transcriptomic and epigenomic data Uses up-to-date methods to exploit omic data Presents methods through specific examples and computing sessions Supplemented by a website, including code, datasets, and solutions |
| 505 0# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | Cover; Half Title; Title Page; Copyright Page; Dedication; Contents; Preface; 1 Introduction; 1.1 Book overview; 1.2 Overview of omic data; 1.2.1 Genomic data; 1.2.1.1 Genomic SNP data; 1.2.1.2 SNP arrays; 1.2.1.3 Sequencing methods; 1.2.2 Genomic data for other structural variants; 1.2.3 Transcriptomic data; 1.2.3.1 Microarrays; 1.2.3.2 RNA-seq; 1.2.4 Epigenomic data; 1.2.5 Exposomic data; 1.3 Association studies; 1.3.1 Genome-wide association studies; 1.3.2 Whole transcriptome pro ling; 1.3.3 Epigenome-wide association studies; 1.3.4 Exposome-wide association studies |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 1.4 Publicly available resources1.4.1 dbGaP; 1.4.2 EGA; 1.4.3 GEO; 1.4.4 1000 Genomes; 1.4.5 GTEx; 1.4.6 TCGA; 1.4.7 Others; 1.5 Bioconductor; 1.5.1 R; 1.5.2 Omic data in Bioconductor; 1.6 Book's outline; 2 Case examples; 2.1 Chapter overview; 2.2 Reproducibility: The case for public data repositories; 2.3 Case 1: dbGaP; 2.4 Case 2: GEO; 2.5 Case 3: GTEx; 2.6 Case 4: TCGA; 2.7 Case 5: NHANES; 3 Dealing with omic data in Bioconductor; 3.1 Chapter overview; 3.2 snpMatrix; 3.3 ExpressionSet; 3.4 SummarizedExperiment; 3.5 GRanges; 3.6 RangedSummarizedExperiment; 3.7 ExposomeSet |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 3.8 MultiAssayExperiment3.9 MultiDataSet; 4 Genetic association studies; 4.1 Chapter overview; 4.2 Genetic association studies; 4.2.1 Analysis packages; 4.2.2 Association tests; 4.2.3 Single SNP analysis; 4.2.4 Hardy{Weinberg equilibrium; 4.2.5 SNP association analysis; 4.2.6 Gene environment and gene gene interactions; 4.3 Haplotype analysis; 4.3.1 Linkage disequilibrium heatmap plots; 4.3.2 Haplotype estimation; 4.3.3 Haplotype association; 4.3.4 Sliding window approach; 4.4 Genetic score; 4.5 Genome-wide association studies; 4.5.1 Quality control of SNPs |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 4.5.2 Quality control of individuals4.5.3 Population ancestry; 4.5.4 Genome-wide association analysis; 4.5.5 Adjusting for population strati cation; 4.6 Post-GWAS visualization and interpretation; 4.6.1 Genome-wide associations for imputed data; 5 Genomic variant studies; 5.1 Chapter overview; 5.2 Copy number variants; 5.2.1 CNV calling; 5.3 Single CNV association; 5.3.1 Inferring copy number status from signal data; 5.3.2 Measuring uncertainty of CNV calling; 5.3.3 Assessing the association between CNVs and traits; 5.3.3.1 Modeling association; 5.3.3.2 Global test of associations |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 5.3.4 Whole genome CNV analysis5.4 Genetic mosaicisms; 5.4.1 Calling genetic mosaicisms; 5.4.2 Calling the loss of chromosome Y; 5.5 Polymorphic inversions; 5.5.1 Inversion detection; 5.5.2 Inversion calling; 5.5.3 Inversion association; 6 Addressing batch e ects; 6.1 Chapter overview; 6.2 SVA; 6.3 ComBat; 7 Transcriptomic studies; 7.1 Chapter overview; 7.2 Microarray data; 7.2.1 Normalization; 7.2.2 Filter; 7.2.3 Di erential expression; 7.3 Next generation sequencing data; 7.3.1 Normalization; 7.3.2 Gene ltering; 7.3.3 Di erential expression; 8 Epigenomic studies; 8.1 Chapter overview |
| 588 ## - | |
| -- | OCLC-licensed vendor bibliographic record. |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Molecular genetics. |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Molecular genetics |
| General subdivision | Data processing. |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Phenotype. |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Gene expression. |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | DNA. |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | R (Computer program language) |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | SCIENCE / Life Sciences / Biochemistry |
| Source of heading or term | bisacsh |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | MATHEMATICS / Probability & Statistics / General |
| Source of heading or term | bisacsh |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | SCIENCE / Life Sciences / Biology / General |
| Source of heading or term | bisacsh |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Cáceres, Alejandro |
| Titles and other words associated with a name | (Bioinformatics researcher), |
| Relator term | author. |
| 856 40 - ELECTRONIC LOCATION AND ACCESS | |
| Materials specified | Taylor & Francis |
| Uniform Resource Identifier | https://www.taylorfrancis.com/books/9780429440557 |
| 856 42 - ELECTRONIC LOCATION AND ACCESS | |
| Materials specified | OCLC metadata license agreement |
| Uniform Resource Identifier | http://www.oclc.org/content/dam/oclc/forms/terms/vbrl-201703.pdf |
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