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wrap biocViews in backticks
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description-file.Rmd

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@@ -192,7 +192,7 @@ package type (i.e., `Software`, `AnnotationData`, `ExperimentData`, or
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`Workflow`). `biocViews` terms are case-sensitive.
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The field name "biocViews" is case-sensitive and must begin with a lower-case
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'b'. Please use a single line with biocViews separated by commas
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'b'. Please use a single line with `biocViews` separated by commas
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(i.e,`biocViews: GeneTarget, SingleCell`).
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important-bioc-features.Rmd

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@@ -6,7 +6,7 @@ Packages added to the _Bioconductor_ Project require a `biocViews:`
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field in their `DESCRIPTION` file. The field name "biocViews" is
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case-sensitive and must begin with a lower-case 'b'.
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biocViews terms are "keywords" used to describe a given package. They
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`biocViews` terms are "keywords" used to describe a given package. They
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are broadly divided into four categories, representing the type of
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packages present in the _Bioconductor_ Project
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3. Experiment Data
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4. Workflow
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biocViews are available for the [release][release-biocviews] and [devel][biocViews] branches of
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_Bioconductor_. The devel branch has a check box under the tree
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structure which, when checked, displays biocViews that are defined but
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not used by any package, in addition to biocViews that are in use. See also
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[description section](#description-biocviews)
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`biocViews` are available for the [release][release-biocviews] and
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[devel][biocViews] branches of _Bioconductor_. The devel branch has a check box
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under the tree structure which, when checked, displays `biocViews` that are
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defined but not used by any package, in addition to `biocViews` that are in use.
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See also [description section](#description-biocviews)
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### Motivation {#biocviews-motivation}
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One can use biocViews for two broad purposes.
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One can use `biocViews` for two broad purposes.
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1. A researcher might want to identify all packages in the
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_Bioconductor_ Project which are related to a specific purpose.
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For example, one may want to look for all packages related to "Copy
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Number Variants".
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2. During development, a package contributor can "tag" their package
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with biocViews so that when someone looking for packages (like in
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with `biocViews` so that when someone looking for packages (like in
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scenario 1) can easily find their package.
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### biocViews during new package development {#biocviews-pkg-devel}
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Visit the ['devel' biocViews][biocViews] when you are in the process of
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adding biocViews to your new package. Identify as many terms as
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adding `biocViews` to your new package. Identify as many terms as
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appropriate from the hierarchy. Prefer 'leaf' terms at the end of the
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hierarchy, over more inclusive terms. Remember to check the box
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displaying all available terms.
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1. Your package will belong to only one part of _Bioconductor_ Project
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(Software, Annotation Data, Experiment Data, Workflow), so choose only
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biocViews from that category.
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`biocViews` from that category.
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2. biocViews listed in your package must match exactly (e.g.,
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spelling, capitalization) the terms in the biocViews hierarchy.
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2. `biocViews` listed in your package must match exactly (e.g.,
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spelling, capitalization) the terms in the `biocViews` hierarchy.
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When you submit your new package for review , your package is checked
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and built by the _Bioconductor_ Project. We check the following for
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biocViews:
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1. Package contributor has added biocViews.
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1. Package contributor has added `biocViews`.
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2. biocViews are valid.
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2. `biocViews` are valid.
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3. Package contributor has added biocViews from only one of the categories.
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3. Package contributor has added `biocViews` from only one of the categories.
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If you receive a "RECOMMENDED" direction for any of these biocViews
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If you receive a "RECOMMENDED" direction for any of these `biocViews`
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after you have submitted your package, you can try correcting them on
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your own following the directions given here or ask your package
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reviewer for more information.
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If a developer thinks a biocViews term should be added to the current acceptable
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list, please email [email protected] requesting the new biocView, under
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which hierarchy the term should be placed, and the justification for the new
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term.
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If a developer thinks a `biocViews` term should be added to the current
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acceptable list, please email <[email protected]> requesting the new
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`biocViews` term, under which hierarchy the term should be placed, and the
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justification for the new term.
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## Common Bioconductor Methods and Classes {#reusebioc}

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