Update JASPAR to 2024 release

moosa-r · Dec 1, 2023 · 56c19ce · 56c19ce
1 parent 01d6b47
commit 56c19ce
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Showing 20 changed files with 395 additions and 419 deletions.
diff --git a/R/internal_functions.R b/R/internal_functions.R
@@ -52,9 +52,9 @@
                    jaspar = switch(
                      arg[[2]],
                      name = "JASPAR",
-                     url = "https://jaspar.genereg.net",
+                     url = "https://jaspar.elixir.no/",
                      pth = "api/v1/",
-                     ptn = "^(https?://)?(www\\.)?jaspar\\.genereg\\.net/api/",
+                     ptn = "^(https?://)?(www\\.)?jaspar\\.elixir\\.no/api/",
                      err_ptn = "^$"
                    ),
                    mieaa = switch(

diff --git a/R/jaspar.R b/R/jaspar.R
diff --git a/README.Rmd b/README.Rmd
@@ -46,7 +46,7 @@ rbioapi is dedicated to **Biological or Medical** databases and web services. Cu
 On CRAN (Stable) version: (<https://cran.r-project.org/package=rbioapi>)
 
 1.  [Enrichr](https://maayanlab.cloud/Enrichr/ "Enrichr") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_enrichr.html "rbioapi & Enrichr vignette article")) ^(new)^
-2.  [JASPAR](https://jaspar.genereg.net/ "JASPAR - A database of transcription factor binding profiles") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html "rbioapi & Enrichr vignette article")) ^(new)^
+2.  [JASPAR](https://jaspar.elixir.no/ "JASPAR - A database of transcription factor binding profiles") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html "rbioapi & Enrichr vignette article")) ^(new)^
 3.  [miEAA](https://ccb-compute2.cs.uni-saarland.de/mieaa2 "miRNA Enrichment Analysis and Annotation Tool (miEAA)") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_mieaa.html "rbioapi & miEAA vignette article"))
 4.  [PANTHER](https://www.pantherdb.org "Protein Analysis THrough Evolutionary Relationships (PANTHER)") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_panther.html "rbioapi & PANTHER vignette article"))
 5.  [Reactome](https://reactome.org/) ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_reactome.html "rbioapi & Reactome vignette article"))
@@ -200,7 +200,7 @@ rbioapi is an interface between you and other databases and services. Thus, if y
 
 -   [How to cite Enrichr](https://rbioapi.moosa-r.com/articles/rbioapi_enrichr.html#citations "How to cite Enrichr"). (See on [Enrichr website](https://maayanlab.cloud/Enrichr/help#terms))
 
--   [How to cite JASPAR](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html#citations "How to cite JASPAR"). (See on [JASPAR website](https://jaspar.genereg.net/faq/))
+-   [How to cite JASPAR](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html#citations "How to cite JASPAR"). (See on [JASPAR website](https://jaspar.elixir.no/faq/))
 
 -   [How to cite miEAA](https://rbioapi.moosa-r.com/articles/rbioapi_mieaa.html#citations "How to cite miEAA"). (See on [miEAA website](https://ccb-compute2.cs.uni-saarland.de/mieaa2))
 

diff --git a/README.md b/README.md
@@ -44,7 +44,7 @@ On CRAN (Stable) version: (<https://cran.r-project.org/package=rbioapi>)
     vignette
     article](https://rbioapi.moosa-r.com/articles/rbioapi_enrichr.html "rbioapi & Enrichr vignette article"))
     <sup>(new)</sup>
-2.  [JASPAR](https://jaspar.genereg.net/ "JASPAR - A database of transcription factor binding profiles")
+2.  [JASPAR](https://jaspar.elixir.no/ "JASPAR - A database of transcription factor binding profiles")
     ([rbioapi vignette
     article](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html "rbioapi & Enrichr vignette article"))
     <sup>(new)</sup>
@@ -339,7 +339,7 @@ used.
 
 - [How to cite
   JASPAR](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html#citations "How to cite JASPAR"). (See on
-  [JASPAR website](https://jaspar.genereg.net/faq/))
+  [JASPAR website](https://jaspar.elixir.no/faq/))
 
 - [How to cite miEAA](https://rbioapi.moosa-r.com/articles/rbioapi_mieaa.html#citations "How to cite miEAA").
   (See on [miEAA

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -90,7 +90,7 @@ reference:
 
 - title: JASPAR (rba_jaspar_*)
   desc: >
-    Functions that connect you to [JASPAR](https://jaspar.genereg.net/)
+    Functions that connect you to [JASPAR](https://jaspar.elixir.no/)
     (Database of transcription factor binding profiles) API resources.
   contents:
     - starts_with("rba_jaspar")

diff --git a/man/rba_jaspar_collections.Rd b/man/rba_jaspar_collections.Rd
diff --git a/man/rba_jaspar_collections_matrices.Rd b/man/rba_jaspar_collections_matrices.Rd
diff --git a/man/rba_jaspar_matrix.Rd b/man/rba_jaspar_matrix.Rd
diff --git a/man/rba_jaspar_matrix_search.Rd b/man/rba_jaspar_matrix_search.Rd
diff --git a/man/rba_jaspar_matrix_versions.Rd b/man/rba_jaspar_matrix_versions.Rd
diff --git a/man/rba_jaspar_releases.Rd b/man/rba_jaspar_releases.Rd