@@ -6,7 +6,7 @@ Packages added to the _Bioconductor_ Project require a `biocViews:`
66field in their ` DESCRIPTION ` file. The field name "biocViews" is
77case-sensitive and must begin with a lower-case 'b'.
88
9- biocViews terms are "keywords" used to describe a given package. They
9+ ` biocViews ` terms are "keywords" used to describe a given package. They
1010are broadly divided into four categories, representing the type of
1111packages present in the _ Bioconductor_ Project
1212
@@ -15,29 +15,29 @@ packages present in the _Bioconductor_ Project
15153 . Experiment Data
16164 . Workflow
1717
18- biocViews are available for the [ release] [ release-biocviews ] and [ devel ] [ biocViews ] branches of
19- _ Bioconductor_ . The devel branch has a check box under the tree
20- structure which, when checked, displays biocViews that are defined but
21- not used by any package, in addition to biocViews that are in use. See also
22- [ description section] ( #description-biocviews )
18+ ` biocViews ` are available for the [ release] [ release-biocviews ] and
19+ [ devel ] [ biocViews ] branches of _ Bioconductor_ . The devel branch has a check box
20+ under the tree structure which, when checked, displays ` biocViews ` that are
21+ defined but not used by any package, in addition to ` biocViews ` that are in use.
22+ See also [ description section] ( #description-biocviews )
2323
2424### Motivation {#biocviews-motivation}
2525
26- One can use biocViews for two broad purposes.
26+ One can use ` biocViews ` for two broad purposes.
2727
28281 . A researcher might want to identify all packages in the
2929 _ Bioconductor_ Project which are related to a specific purpose.
3030 For example, one may want to look for all packages related to "Copy
3131 Number Variants".
3232
33332 . During development, a package contributor can "tag" their package
34- with biocViews so that when someone looking for packages (like in
34+ with ` biocViews ` so that when someone looking for packages (like in
3535 scenario 1) can easily find their package.
3636
3737### biocViews during new package development {#biocviews-pkg-devel}
3838
3939Visit the [ 'devel' biocViews] [ biocViews ] when you are in the process of
40- adding biocViews to your new package. Identify as many terms as
40+ adding ` biocViews ` to your new package. Identify as many terms as
4141appropriate from the hierarchy. Prefer 'leaf' terms at the end of the
4242hierarchy, over more inclusive terms. Remember to check the box
4343displaying all available terms.
@@ -46,30 +46,30 @@ Please Note:
4646
47471 . Your package will belong to only one part of _ Bioconductor_ Project
4848 (Software, Annotation Data, Experiment Data, Workflow), so choose only
49- biocViews from that category.
49+ ` biocViews ` from that category.
5050
51- 2 . biocViews listed in your package must match exactly (e.g.,
52- spelling, capitalization) the terms in the biocViews hierarchy.
51+ 2 . ` biocViews ` listed in your package must match exactly (e.g.,
52+ spelling, capitalization) the terms in the ` biocViews ` hierarchy.
5353
5454When you submit your new package for review , your package is checked
5555and built by the _ Bioconductor_ Project. We check the following for
5656biocViews:
5757
58- 1 . Package contributor has added biocViews.
58+ 1 . Package contributor has added ` biocViews ` .
5959
60- 2 . biocViews are valid.
60+ 2 . ` biocViews ` are valid.
6161
62- 3 . Package contributor has added biocViews from only one of the categories.
62+ 3 . Package contributor has added ` biocViews ` from only one of the categories.
6363
64- If you receive a "RECOMMENDED" direction for any of these biocViews
64+ If you receive a "RECOMMENDED" direction for any of these ` biocViews `
6565after you have submitted your package, you can try correcting them on
6666your own following the directions given here or ask your package
6767reviewer for more information.
6868
69- If a developer thinks a biocViews term should be added to the current acceptable
70- list, please email
[email protected] requesting the new
biocView, under 71- which hierarchy the term should be placed, and the justification for the new
72- term.
69+ If a developer thinks a ` biocViews ` term should be added to the current
70+ acceptable list, please email
< [email protected] > requesting the new
71+ ` biocViews ` term, under which hierarchy the term should be placed, and the
72+ justification for the new term.
7373
7474
7575## Common Bioconductor Methods and Classes {#reusebioc}
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