update DESCRIPTION, remove unneeded comments from vignette

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 = "[email protected]", role = c("aut", "cre")),
     person("Hervé", " Pagès", email = "[email protected]", role = c("aut")),

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
 
-<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
+- **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].
-    <br/>
-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)
+```

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.