additional improvements

- convert list to table

Author: LiNk-NY

bioc-classes-methods.Rmd

@@ -5,15 +5,15 @@
 Bioconductor is a large and diverse project with many packages that provide
 functionality for a wide range of biological data types and statistical methods.
 It has a rich set of classes and methods that are widely used across
-many packages. It, therefore, is important to reuse existing data classes and
+many packages. It is, therefore, important to reuse existing data classes and
 methods to ensure that packages are inter-operable with the rest of the
-_Bioconductor_ ecosystem. Central data representations allow users to readily
-integrate analysis workflows across multiple Bioconductor packages providing a
-more seamless user experience.
+_Bioconductor_ software ecosystem. Central data representations allow users to
+readily integrate analysis workflows across multiple Bioconductor packages
+providing a more seamless user experience.
 
 Many classes in Bioconductor are implemented using the S4 object-oriented
 system in R. The S4 system is particularly well-suited for the representation
-of complex genomic data structures and the initial motivations to use S4 in
+of complex genomic data structures. The initial motivations to use S4 in
 Bioconductor were centered around its benefits over other systems such as S3.
 These benefits include, but are not limited to, formal class definitions,
 multiple inheritance, and validity checking.
@@ -41,12 +41,12 @@ commonly used packages and their methods to import various data types:
 This list is not exhaustive, and developers are encouraged to initiate dialogue
 with other community members to identify additional packages and methods that
 may be useful for their specific use case. We acknowledge that class and method
-discover-ability can be a challenge and we are working to improve this aspect of
+discoverability can be a challenge and we are working to improve this aspect of
 the Bioconductor project.
 
 ### Common Classes {#commonclass}
 
-The following list, though not exhaustive, provides select classes and
+The following list, though certainly not exhaustive, provides select classes and
 constructor functions to represent genomic data:
 
 + Rectangular feature x sample data --
@@ -75,32 +75,24 @@ package.
 
 ## Package Submission Considerations
 
-Bioconductor strives for interoperability across packages. To ensure this, we
-strongly encourage that package submissions reuse existing Bioconductor classes
-and methods. Packages that do not follow this guideline may be asked to revise
+Bioconductor strives for interoperability across packages and strongly
+encourages that package submissions reuse existing Bioconductor classes and
+methods. Packages that do not follow this guideline may be asked to revise
 their code to use existing classes and methods.
 
 In the case where the data does not conform to an existing data class,
 we recommend discussing the design of a new class with the Bioconductor
 community. The open discussion can take place on main Bioconductor communication
 channels such as the [bioc-devel][bioc-devel-mail] mailing list, or the
-Bioconductor slack.
+Bioconductor community slack.
 
 ## Package Implementations
 
-The following packages are examples of packages that have reused Bioconductor
-classes and methods:
-
-+ `r BiocStyle::Biocpkg("DESeq2")` --
-  Uses `r BiocStyle::Biocpkg("SummarizedExperiment")` and
-  `r BiocStyle::Biocpkg("GenomicRanges")`
-+ `r BiocStyle::Biocpkg("GenomicAlignments")` --
-  Uses `r BiocStyle::Biocpkg("GenomicRanges")` and
-  `r BiocStyle::Biocpkg("Rsamtools")`
-+ `r BiocStyle::Biocpkg("VariantAnnotation")` --
-  Uses `r BiocStyle::Biocpkg("GenomicRanges")`,
-  `r BiocStyle::Biocpkg("SummarizedExperiment")`, and
-  `r BiocStyle::Biocpkg("Rsamtools")` classes.
-  
-  
-  
+The following packages are examples of packages that reuse Bioconductor classes
+and methods:
+
+| package | inherits classes and methods from: |
+|---|---|
+| `r BiocStyle::Biocpkg("DESeq2")` | `r BiocStyle::Biocpkg("SummarizedExperiment")`, `r BiocStyle::Biocpkg("GenomicRanges")` |
+| `r BiocStyle::Biocpkg("GenomicAlignments")` | `r BiocStyle::Biocpkg("GenomicRanges")`, `r BiocStyle::Biocpkg("Rsamtools")` |
+| `r BiocStyle::Biocpkg("VariantAnnotation")` | `r BiocStyle::Biocpkg("GenomicRanges")`, `r BiocStyle::Biocpkg("SummarizedExperiment")`, `r BiocStyle::Biocpkg("Rsamtools")` |