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Workshop description

In this workshop, we will learn about Bioconductor data containers that use lazy data representations and about their application in real data analysis. We will use some real data examples generated from DNA/RNA-seq, to demonstrate the representation and comprehension of large scale (out-of-memory) genomic datasets. The workshop will be mainly instructor-led live demo with completely working examples. Instructions and notes will be included.

Instructors and contact information

  • Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY

Pre-requisites

  • Basic knowledge of R syntax (matrix, array, data.frame, etc.)
  • Some familiarity with manipulation of S4 objects in general
  • Some familiarity with SummarizedExperiment objects

Learning objectives

  • Introduction to DelayedArray objects and related concepts (seed, delayed operations, realization, block-processed operations, in-memory vs on-disk backends, etc...)

  • Use VariantExperiment to represent your DNA-seq data.

  • Statistical analysis of variant data (VCF) using VariantExperiment.

  • Create SQLDataFrame from in-memory data, text format file, and database tables.

  • Use SQLDataFrame to represent and manipulate orgdb database tables.

Workshop participation

Students will be using their laptops with internet connection, follow the instructor to read course materials and run through the working code chunks.

Time outline

ActivityTime
DelayedArray and HDF5Array objects30m
DelayedArray and HDF5Array hands-on10m
Specialized DelayedArray backends10m
VariantExperiment20m
DelayedDataFrame10m
SQLDataFrame10m
Future directions5-10m

R/Bioconductor packages

The workshop makes use of the following packages:

library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)

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Workshop description
In this workshop, we will learn about Bioconductor data containers that
use lazy data representations and about their application in real data
analysis. We will use some real data examples generated from DNA/RNA-seq,
to demonstrate the representation and comprehension of large scale
(out-of-memory) genomic datasets. The workshop will be mainly instructor-led
live demo with completely working examples. Instructions and notes will be
included.
Instructors and contact information
  • Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY
Pre-requisites
  • Basic knowledge of R syntax (matrix, array, data.frame, etc.)
  • Some familiarity with manipulation of S4 objects in general
  • Some familiarity with SummarizedExperiment objects
Learning objectives
  • Introduction to DelayedArray objects and related concepts (seed,
delayed operations, realization, block-processed operations, in-memory
vs on-disk backends, etc...)
  • Use VariantExperiment to represent your DNA-seq data.
  • Statistical analysis of variant data (VCF) using VariantExperiment.
  • Create SQLDataFrame from in-memory data, text format file, and
database tables.
  • Use SQLDataFrame to represent and manipulate orgdb database tables.
Workshop participation
Students will be using their laptops with internet connection, follow
the instructor to read course materials and run through the working
code chunks.
Time outline
ActivityTime
DelayedArray and HDF5Array objects30m
DelayedArray and HDF5Array hands-on10m
Specialized DelayedArray backends10m
VariantExperiment20m
DelayedDataFrame10m
SQLDataFrame10m
Future directions5-10m
R/Bioconductor packages
The workshop makes use of the following packages:
library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)

About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
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Workshop description
In this workshop, we will learn about Bioconductor data containers that
use lazy data representations and about their application in real data
analysis. We will use some real data examples generated from DNA/RNA-seq,
to demonstrate the representation and comprehension of large scale
(out-of-memory) genomic datasets. The workshop will be mainly instructor-led
live demo with completely working examples. Instructions and notes will be
included.
Instructors and contact information
  • Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY
Pre-requisites
  • Basic knowledge of R syntax (matrix, array, data.frame, etc.)
  • Some familiarity with manipulation of S4 objects in general
  • Some familiarity with SummarizedExperiment objects
Learning objectives
  • Introduction to DelayedArray objects and related concepts (seed,
delayed operations, realization, block-processed operations, in-memory
vs on-disk backends, etc...)
  • Use VariantExperiment to represent your DNA-seq data.
  • Statistical analysis of variant data (VCF) using VariantExperiment.
  • Create SQLDataFrame from in-memory data, text format file, and
database tables.
  • Use SQLDataFrame to represent and manipulate orgdb database tables.
Workshop participation
Students will be using their laptops with internet connection, follow
the instructor to read course materials and run through the working
code chunks.
Time outline
ActivityTime
DelayedArray and HDF5Array objects30m
DelayedArray and HDF5Array hands-on10m
Specialized DelayedArray backends10m
VariantExperiment20m
DelayedDataFrame10m
SQLDataFrame10m
Future directions5-10m
R/Bioconductor packages
The workshop makes use of the following packages:
library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)

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README.md
Repository files navigation
Workshop description
In this workshop, we will learn about Bioconductor data containers that
use lazy data representations and about their application in real data
analysis. We will use some real data examples generated from DNA/RNA-seq,
to demonstrate the representation and comprehension of large scale
(out-of-memory) genomic datasets. The workshop will be mainly instructor-led
live demo with completely working examples. Instructions and notes will be
included.
Instructors and contact information
  • Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY
Pre-requisites
  • Basic knowledge of R syntax (matrix, array, data.frame, etc.)
  • Some familiarity with manipulation of S4 objects in general
  • Some familiarity with SummarizedExperiment objects
Learning objectives
  • Introduction to DelayedArray objects and related concepts (seed,
delayed operations, realization, block-processed operations, in-memory
vs on-disk backends, etc...)
  • Use VariantExperiment to represent your DNA-seq data.
  • Statistical analysis of variant data (VCF) using VariantExperiment.
  • Create SQLDataFrame from in-memory data, text format file, and
database tables.
  • Use SQLDataFrame to represent and manipulate orgdb database tables.
Workshop participation
Students will be using their laptops with internet connection, follow
the instructor to read course materials and run through the working
code chunks.
Time outline
ActivityTime
DelayedArray and HDF5Array objects30m
DelayedArray and HDF5Array hands-on10m
Specialized DelayedArray backends10m
VariantExperiment20m
DelayedDataFrame10m
SQLDataFrame10m
Future directions5-10m
R/Bioconductor packages
The workshop makes use of the following packages:
library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)

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Workshop description
In this workshop, we will learn about Bioconductor data containers that
use lazy data representations and about their application in real data
analysis. We will use some real data examples generated from DNA/RNA-seq,
to demonstrate the representation and comprehension of large scale
(out-of-memory) genomic datasets. The workshop will be mainly instructor-led
live demo with completely working examples. Instructions and notes will be
included.
Instructors and contact information
  • Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY
Pre-requisites
  • Basic knowledge of R syntax (matrix, array, data.frame, etc.)
  • Some familiarity with manipulation of S4 objects in general
  • Some familiarity with SummarizedExperiment objects
Learning objectives
  • Introduction to DelayedArray objects and related concepts (seed,
delayed operations, realization, block-processed operations, in-memory
vs on-disk backends, etc...)
  • Use VariantExperiment to represent your DNA-seq data.
  • Statistical analysis of variant data (VCF) using VariantExperiment.
  • Create SQLDataFrame from in-memory data, text format file, and
database tables.
  • Use SQLDataFrame to represent and manipulate orgdb database tables.
Workshop participation
Students will be using their laptops with internet connection, follow
the instructor to read course materials and run through the working
code chunks.
Time outline
ActivityTime
DelayedArray and HDF5Array objects30m
DelayedArray and HDF5Array hands-on10m
Specialized DelayedArray backends10m
VariantExperiment20m
DelayedDataFrame10m
SQLDataFrame10m
Future directions5-10m
R/Bioconductor packages
The workshop makes use of the following packages:
library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)

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Workshop description
In this workshop, we will learn about Bioconductor data containers that
use lazy data representations and about their application in real data
analysis. We will use some real data examples generated from DNA/RNA-seq,
to demonstrate the representation and comprehension of large scale
(out-of-memory) genomic datasets. The workshop will be mainly instructor-led
live demo with completely working examples. Instructions and notes will be
included.
Instructors and contact information
  • Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY
Pre-requisites
  • Basic knowledge of R syntax (matrix, array, data.frame, etc.)
  • Some familiarity with manipulation of S4 objects in general
  • Some familiarity with SummarizedExperiment objects
Learning objectives
  • Introduction to DelayedArray objects and related concepts (seed,
delayed operations, realization, block-processed operations, in-memory
vs on-disk backends, etc...)
  • Use VariantExperiment to represent your DNA-seq data.
  • Statistical analysis of variant data (VCF) using VariantExperiment.
  • Create SQLDataFrame from in-memory data, text format file, and
database tables.
  • Use SQLDataFrame to represent and manipulate orgdb database tables.
Workshop participation
Students will be using their laptops with internet connection, follow
the instructor to read course materials and run through the working
code chunks.
Time outline
ActivityTime
DelayedArray and HDF5Array objects30m
DelayedArray and HDF5Array hands-on10m
Specialized DelayedArray backends10m
VariantExperiment20m
DelayedDataFrame10m
SQLDataFrame10m
Future directions5-10m
R/Bioconductor packages
The workshop makes use of the following packages:
library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)

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The official repository of the Bioconductor 2019 Conference Workshops 🎊
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Workshop description
In this workshop, we will learn about Bioconductor data containers that
use lazy data representations and about their application in real data
analysis. We will use some real data examples generated from DNA/RNA-seq,
to demonstrate the representation and comprehension of large scale
(out-of-memory) genomic datasets. The workshop will be mainly instructor-led
live demo with completely working examples. Instructions and notes will be
included.
Instructors and contact information
  • Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY
Pre-requisites
  • Basic knowledge of R syntax (matrix, array, data.frame, etc.)
  • Some familiarity with manipulation of S4 objects in general
  • Some familiarity with SummarizedExperiment objects
Learning objectives
  • Introduction to DelayedArray objects and related concepts (seed,
delayed operations, realization, block-processed operations, in-memory
vs on-disk backends, etc...)
  • Use VariantExperiment to represent your DNA-seq data.
  • Statistical analysis of variant data (VCF) using VariantExperiment.
  • Create SQLDataFrame from in-memory data, text format file, and
database tables.
  • Use SQLDataFrame to represent and manipulate orgdb database tables.
Workshop participation
Students will be using their laptops with internet connection, follow
the instructor to read course materials and run through the working
code chunks.
Time outline
ActivityTime
DelayedArray and HDF5Array objects30m
DelayedArray and HDF5Array hands-on10m
Specialized DelayedArray backends10m
VariantExperiment20m
DelayedDataFrame10m
SQLDataFrame10m
Future directions5-10m
R/Bioconductor packages
The workshop makes use of the following packages:
library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)

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Workshop description
In this workshop, we will learn about Bioconductor data containers that
use lazy data representations and about their application in real data
analysis. We will use some real data examples generated from DNA/RNA-seq,
to demonstrate the representation and comprehension of large scale
(out-of-memory) genomic datasets. The workshop will be mainly instructor-led
live demo with completely working examples. Instructions and notes will be
included.
Instructors and contact information
  • Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
  • Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
  • Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY
Pre-requisites
  • Basic knowledge of R syntax (matrix, array, data.frame, etc.)
  • Some familiarity with manipulation of S4 objects in general
  • Some familiarity with SummarizedExperiment objects
Learning objectives
  • Introduction to DelayedArray objects and related concepts (seed,
delayed operations, realization, block-processed operations, in-memory
vs on-disk backends, etc...)
  • Use VariantExperiment to represent your DNA-seq data.
  • Statistical analysis of variant data (VCF) using VariantExperiment.
  • Create SQLDataFrame from in-memory data, text format file, and
database tables.
  • Use SQLDataFrame to represent and manipulate orgdb database tables.
Workshop participation
Students will be using their laptops with internet connection, follow
the instructor to read course materials and run through the working
code chunks.
Time outline
ActivityTime
DelayedArray and HDF5Array objects30m
DelayedArray and HDF5Array hands-on10m
Specialized DelayedArray backends10m
VariantExperiment20m
DelayedDataFrame10m
SQLDataFrame10m
Future directions5-10m
R/Bioconductor packages
The workshop makes use of the following packages:
library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)

About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
Resources
Readme
Activity
Stars
2 stars
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1 watching
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Contributors