From 582014103e1a1c485c70675786689411c33fc3f2 Mon Sep 17 00:00:00 2001 From: qian Date: Thu, 1 Aug 2019 12:02:48 -0400 Subject: [PATCH] update DESCRIPTION, remove unneeded comments from vignette --- DESCRIPTION | 6 +- README.md | 104 +++++++++++------------ vignettes/Bioc_201_herveQian_LazyRep.Rmd | 3 +- 3 files changed, 56 insertions(+), 57 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8f5322e..10d43cc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,9 +1,9 @@ -Package: BiocWorkshops2019 +Package: BiocLazyRep Type: Package Encoding: UTF-8 Title: Bioconductor 2019 Conference Workshops -Version: 3.9.1 -Description: Lazy representation of very large genomic Data resources in R/Bioconductor +Version: 0.0.2 +Description: Lazy representation of very large genomic Data resources in R/Bioconductor. Authors@R: c( person("Qian", "Liu", email = "qian.liu@roswellpark.org", role = c("aut", "cre")), person("Hervé", " Pagès", email = "hpages@fredhutch.org", role = c("aut")), diff --git a/README.md b/README.md index f177666..ca88180 100644 --- a/README.md +++ b/README.md @@ -1,72 +1,72 @@ ---- -knit: "bookdown::render_book" -title: "The Bioconductor 2019 Workshops Repository" -description: "This book is a central repository for all the workshops submitted to the Bioconductor 2019 Conference" -site: bookdown::bookdown_site -github-repo: Bioconductor/BiocWorkshops2019 -documentclass: book ---- +### Instructors and contact information -Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License. +- **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 -# Introduction -Author: - Martin Morgan^[Roswell Park Comprehensive Cancer Center, Buffalo, NY]. -
-Last modified: May 23, 2019 +### Pre-requisites -## For Everyone +- Basic knowledge of R syntax (`matrix`, `array`, `data.frame`, etc.) +- Some familiarity with manipulation of S4 objects in general +- Some familiarity with `SummarizedExperiment` objects -This book contains workshops used in _R_ / _Bioconductor_ -training. The workshops are divided into 3 sections: -- **Learn** (100-series chapters) contains material for beginning - users of _R_ and _Bioconductor_. The _Bioconductor_-related material - is relevant even for experienced _R_ users who are new to - _Bioconductor_. +### Learning objectives -- **Use** (200-series chapters) contains workshops emphasizing use of - _Bioconductor_ for common tasks, e.g., bulk RNA-seq differential - expression, ChIP-seq, single-cell analysis, gene set enrichment, and - annotation. +- Introduction to `DelayedArray` objects and related concepts (seed, + delayed operations, realization, block-processed operations, in-memory + vs on-disk backends, etc...) -- **Develop** (500-series chapters) contains workshops to help expert - users hone their skills and contribute their domain-specific - knowledge to the _Bioconductor_ community. +- Use `VariantExperiment` to represent your DNA-seq data. -## For Workshop Authors +- Statistical analysis of variant data (VCF) using `VariantExperiment`. -To contribute a new workshop, open a [BiocWorkshops issue][] starting with -the `[Workshop]` keyword in the title of the issue. Provide a link to the -repository in the issue message body. You may also include GitHub usernames -of workshop collaborators. For a successful workshop build, adhere to the -following: +- Create `SQLDataFrame` from in-memory data, text format file, and + database tables. -1. Package your workshop as an R package -2. Include a standard vignette in the vignettes directory -3. Put any extra files (images, .bib) in `inst/vignettes` and reference them -in the vignette using `system.file` -4. Number **3** requires package chapter installation before vignette build or -`build_vignettes=TRUE` when building the package. +- Use `SQLDataFrame` to represent and manipulate orgdb database tables. -### DESCRIPTION -Update the DESCRIPTION file adding packages utilized in your workshop to -the **Imports** field. +### Workshop participation -### Classifying your workshop +Students will be using their laptops with internet connection, follow +the instructor to read course materials and run through the working +code chunks. -Follow the numbering scheme above to classify your workshop by preceding your title with -"Bioconductor 1xx:", "Bioconductor 2xx:", or "Bioconductor 5xx:". Final workshop numbers will be -determined by an editor. -## Deadlines for Bioc2019 +### Time outline -Please be aware of the following deadlines for the [Bioconductor 2019 Conference][] in New York +| Activity | Time | +|----------|------| +| DelayedArray and HDF5Array objects | 30m | +| DelayedArray and HDF5Array hands-on | 10m | +| Specialized DelayedArray backends | 10m | +| VariantExperiment | 20m | +| DelayedDataFrame | 10m | +| SQLDataFrame | 10m | +| Future directions | 5-10m | -- **Mon May 27:** draft workshop materials submitted to this Bioconductor GitHub repo as a pull request -[BiocWorkshops issue]: https://github.com/Bioconductor/BiocWorkshops2019/issues -[Bioconductor 2019 Conference]: https://bioc2019.bioconductor.org/ +### _R/Bioconductor_ packages +The workshop makes use of the following packages: + +```{r setup, message = FALSE} +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) +``` diff --git a/vignettes/Bioc_201_herveQian_LazyRep.Rmd b/vignettes/Bioc_201_herveQian_LazyRep.Rmd index 823cb6a..940cb72 100644 --- a/vignettes/Bioc_201_herveQian_LazyRep.Rmd +++ b/vignettes/Bioc_201_herveQian_LazyRep.Rmd @@ -654,8 +654,7 @@ gf$annotation$info gf$annotation$info$AC ``` Try typing in `gf$ann` and pressing tab key for the -auto-completion. (Changes made in GDSArray, wait for new build -tomorrow June 7th.) +auto-completion. `gdsfile()` function returns the file path of the corresponding GDS file.