Bioconductor Code: OmnipathR

Graph of OmnipathR

a224a9a (HEAD -> devel, origin/master, origin/devel, origin/HEAD) Bump version: 3.11.0 → 3.11.1 by deeenes <turei.denes@gmail.com> 2023-10-25 17:49:17 +0200;
33cd926 merging BioC version bump & fork of 3.19 devel by deeenes <turei.denes@gmail.com> 2023-10-25 17:49:07 +0200;
b1b2bab (origin/RELEASE_3_18, RELEASE_3_18) Bump version: 3.10.0 → 3.10.1 by deeenes <turei.denes@gmail.com> 2023-10-25 17:47:10 +0200;
2b5c820 merging `devel` (last fixes around release) by deeenes <turei.denes@gmail.com> 2023-10-25 17:46:46 +0200;
e65fa1b merging `master` by deeenes <turei.denes@gmail.com> 2023-10-25 17:41:31 +0200;
472611e Bump version: 3.9.10 → 3.9.11 by deeenes <turei.denes@gmail.com> 2023-10-25 17:40:20 +0200;
24a665d `static`: added missing NSE vs R CMD check variable definitions by deeenes <turei.denes@gmail.com> 2023-10-25 17:38:50 +0200;
379dc74 `cookie`: added params missing from docs by deeenes <turei.denes@gmail.com> 2023-10-25 17:38:08 +0200;
39bb1e7 Bump version: 3.9.9 → 3.9.10 by deeenes <turei.denes@gmail.com> 2023-10-25 17:39:00 +0200;
e5505ae `static`: added missing NSE vs R CMD check variable definitions by deeenes <turei.denes@gmail.com> 2023-10-25 17:38:50 +0200;
547b0de `cookie`: added params missing from docs by deeenes <turei.denes@gmail.com> 2023-10-25 17:38:08 +0200;
f898993 docs: missing return values by deeenes <turei.denes@gmail.com> 2023-10-25 13:33:22 +0200;
347eb58 Bump version: 3.9.9 → 3.9.10 by deeenes <turei.denes@gmail.com> 2023-10-25 13:19:45 +0200;
c70ae07 added `stringi` to `Imports` by deeenes <turei.denes@gmail.com> 2023-10-25 13:15:23 +0200;
2ed93a5 added `stringi` to `Imports` by deeenes <turei.denes@gmail.com> 2023-10-25 13:15:23 +0200;
3d812e0 bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 11:17:18 -0400;
636b30c bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 11:17:18 -0400;
7ab2ce9 Merge branch 'master' into devel by deeenes <turei.denes@gmail.com> 2023-10-20 14:28:26 +0200;
c4ce845 Bump version: 3.9.8 → 3.9.9 by deeenes <turei.denes@gmail.com> 2023-10-20 14:27:56 +0200;
b66126a missing NSE vs R CMD check workarounds by deeenes <turei.denes@gmail.com> 2023-10-20 14:27:40 +0200;
98117cf encode URLs for OmniPath queries by deeenes <turei.denes@gmail.com> 2023-10-04 15:26:26 +0200;
f72c23b I thought `OmnipathR` already accepts organism names saezlab/CollecTRI@707f0b8 by deeenes <turei.denes@gmail.com> 2023-10-03 18:02:00 +0200;
21d7b9a `static_table`: fixed handling of organism by deeenes <turei.denes@gmail.com> 2023-09-18 22:59:18 +0200;
cc7636e Bump version: 3.9.7 → 3.9.8 by deeenes <turei.denes@gmail.com> 2023-09-18 22:37:33 +0200;
2a8aeb7 `cache` was missing from the parameter names for `import_omnipath` by deeenes <turei.denes@gmail.com> 2023-09-18 22:35:08 +0200;
c03aac5 `static_tables`: use simply `curl_fetch_memory` (also bypassing cache) by deeenes <turei.denes@gmail.com> 2023-09-17 15:46:36 +0200;
bf130e0 `use_cache`: option to disable the cache by deeenes <turei.denes@gmail.com> 2023-09-17 15:30:32 +0200;
569b25a website: reference rebuild by deeenes <turei.denes@gmail.com> 2023-09-17 01:17:35 +0200;
0999466 new doc pages by deeenes <turei.denes@gmail.com> 2023-09-17 01:17:21 +0200;
482bba2 `static_table`: retrieve one static table from OmniPath by deeenes <turei.denes@gmail.com> 2023-09-17 00:23:25 +0200;
a1441f9 OmniPath static no-TLS URL by deeenes <turei.denes@gmail.com> 2023-09-17 00:23:05 +0200;
3c10b20 `omnipath_download` adds the URL to the attributes of the returned object by deeenes <turei.denes@gmail.com> 2023-09-17 00:22:35 +0200;
8b9858c moved adding the query type specific message into new function by deeenes <turei.denes@gmail.com> 2023-09-17 00:22:08 +0200;
9871d07 separated OmniPath post processing into a new function by deeenes <turei.denes@gmail.com> 2023-09-17 00:21:10 +0200;
3c856a6 `static_tables`: list static tables from OmniPath by deeenes <turei.denes@gmail.com> 2023-09-16 19:50:33 +0200;
b12b9bf (origin/RELEASE_3_17, RELEASE_3_17) docs rebuild by deeenes <turei.denes@gmail.com> 2023-09-15 14:58:47 +0200;
ae9707b Bump version: 3.8.1 → 3.8.2 by deeenes <turei.denes@gmail.com> 2023-09-15 14:58:04 +0200;
7afd93a backported the transition to the new UniProt API by deeenes <turei.denes@gmail.com> 2023-06-06 23:58:57 +0200;
a59fc86 dontrun for most of the evidences related doc examples by deeenes <turei.denes@gmail.com> 2023-06-01 20:10:17 +0200;
ed0973d `translate_ids`: handle organism also as named arg by deeenes <turei.denes@gmail.com> 2023-06-01 20:00:10 +0200;
2f70aff `translate_ids`: adjustment to dplyr api change by deeenes <turei.denes@gmail.com> 2023-06-01 19:59:43 +0200;
e4c8fa4 `simplify = FALSE` when unnesting evidences by deeenes <turei.denes@gmail.com> 2023-06-01 18:29:18 +0200;
613800d removed huge output from docs of `database_summary` by deeenes <turei.denes@gmail.com> 2023-09-14 23:05:26 +0200;
7d148f9 `dplyr` has to be `>= 1.1.0` due to `join_by` by deeenes <turei.denes@gmail.com> 2023-09-12 22:52:09 +0200;
73dca2e `cookie`: generic function to deal with http cookies by deeenes <turei.denes@gmail.com> 2023-09-12 22:31:59 +0200;
b5dac82 Bump version: 3.9.6 → 3.9.7 by deeenes <turei.denes@gmail.com> 2023-09-12 16:15:30 +0200;
d11d5ce automatic fallback to no-TLS (plain http) for omnipath URLs by deeenes <turei.denes@gmail.com> 2023-09-12 16:15:15 +0200;
97d950b website rebuild by deeenes <turei.denes@gmail.com> 2023-09-12 14:40:10 +0200;
8e94833 web site rebuild by deeenes <turei.denes@gmail.com> 2023-06-22 13:53:33 +0200;
7231b89 updated URL and field label in doc example for `all_uniprots` by deeenes <turei.denes@gmail.com> 2023-06-22 13:52:06 +0200;
0e51391 clarifications in docs according to <a href="#74">#74</a> by deeenes <turei.denes@gmail.com> 2023-06-22 12:02:55 +0200;
19fc47c Bump version: 3.9.5 → 3.9.6 by deeenes <turei.denes@gmail.com> 2023-06-08 23:20:57 +0200;
95699f2 missing imported function `dplyr::join_by` by deeenes <turei.denes@gmail.com> 2023-06-08 23:20:51 +0200;
0e730d0 Bump version: 3.9.4 → 3.9.5 by deeenes <turei.denes@gmail.com> 2023-06-08 21:01:06 +0200;
f2f8cee replaced legacy `uploadlists` with new `id-mapping` API by deeenes <turei.denes@gmail.com> 2023-06-08 20:38:59 +0200;
8a7bada `urls`: new UniProt ID mapping API URLs by deeenes <turei.denes@gmail.com> 2023-06-08 20:37:29 +0200;
d5e62f3 `id_types`: updated to new UniProt ID Mapping API by deeenes <turei.denes@gmail.com> 2023-06-08 20:36:39 +0200;
3989c7d `download_to_cache` - include POST fields in cache key by deeenes <turei.denes@gmail.com> 2023-06-08 20:35:59 +0200;
1853341 adjusted ID mapping to new UniProt REST API by deeenes <turei.denes@gmail.com> 2023-06-07 00:48:34 +0200;
d1c5e6e new UniProt REST API field names by deeenes <turei.denes@gmail.com> 2023-06-07 00:43:27 +0200;
c217814 `all_uniprots` uses the new UniProt REST API by deeenes <turei.denes@gmail.com> 2023-06-06 23:58:57 +0200;
ce0fad9 Bump version: 3.9.3 → 3.9.4 by deeenes <turei.denes@gmail.com> 2023-06-01 20:12:23 +0200;
da8b711 dontrun for most of the evidences related doc examples by deeenes <turei.denes@gmail.com> 2023-06-01 20:10:17 +0200;
38ff958 `translate_ids`: handle organism also as named arg by deeenes <turei.denes@gmail.com> 2023-06-01 20:00:10 +0200;
c00046f `translate_ids`: adjustment to dplyr api change by deeenes <turei.denes@gmail.com> 2023-06-01 19:59:43 +0200;
74a0e97 `simplify = FALSE` when unnesting evidences by deeenes <turei.denes@gmail.com> 2023-06-01 18:29:18 +0200;
7a3c0de pkgdown site rebuild by deeenes <turei.denes@gmail.com> 2023-05-22 18:47:55 +0200;
0181c62 Bump version: 3.9.2 → 3.9.3 by deeenes <turei.denes@gmail.com> 2023-05-22 18:29:58 +0200;
9deb4af Bump version: 3.8.0 → 3.8.1 by deeenes <turei.denes@gmail.com> 2023-05-22 18:29:00 +0200;
0c21d32 updated bumpversion to BioC release version by deeenes <turei.denes@gmail.com> 2023-05-22 18:28:55 +0200;
89bdd7d backport "evidences" feature from `devel`: maintain compatibility with the server and dependent packages by deeenes <turei.denes@gmail.com> 2023-05-21 00:30:28 +0200;
46f4983 nothing by deeenes <turei.denes@gmail.com> 2023-05-22 18:04:58 +0200;
1596d25 added `strict_evidences` to docs and argument lists for all interactions query functions by deeenes <turei.denes@gmail.com> 2023-05-22 17:21:22 +0200;
9950561 `strict_evidences = TRUE` is default for `collectri` and `dorothea` by deeenes <turei.denes@gmail.com> 2023-05-22 17:20:49 +0200;
742af62 `from_evidences`: recreate also `n_re*` columns by deeenes <turei.denes@gmail.com> 2023-05-22 16:43:04 +0200;
3061d19 NSE vs. R CMD check workarounds in `evidences.R` by deeenes <turei.denes@gmail.com> 2023-05-22 16:42:28 +0200;
1c32953 more docstrings for `evidences` functions: details, examples, etc. + exporting `from_evidences` by deeenes <turei.denes@gmail.com> 2023-05-22 16:09:55 +0200;
766f080 `from_evidences`: recreate also consensus columns and curation effort by deeenes <turei.denes@gmail.com> 2023-05-22 16:09:09 +0200;
6c41e53 `evidences`: always sort character vectors (sources, references) before concatenating by deeenes <turei.denes@gmail.com> 2023-05-22 14:33:16 +0200;
fdaebef `evidences`: fixed 3 errors in one `select` statement by deeenes <turei.denes@gmail.com> 2023-05-22 14:32:31 +0200;
e16db76 `evidences`: log message also about filtering evidences by deeenes <turei.denes@gmail.com> 2023-05-22 14:31:46 +0200;
7afa6cc always include `evidences` column if `strict_evidences` is `TRUE` by deeenes <turei.denes@gmail.com> 2023-05-22 14:30:59 +0200;
d1f0ffc call `only_from` in `donwload_omnipath` depending on new argument `strict_evidences` by deeenes <turei.denes@gmail.com> 2023-05-22 07:51:39 +0200;
15f56c7 log message in `only_from` by deeenes <turei.denes@gmail.com> 2023-05-22 07:50:20 +0200;
7ac3b81 `only_from` & `filter_evidences`: reconstitute interaction records from evidences by deeenes <turei.denes@gmail.com> 2023-05-22 06:37:16 +0200;
430f999 `must_have_evidences`: check and throw error before all methods that operate on the `evidences` column by deeenes <turei.denes@gmail.com> 2023-05-21 21:45:13 +0200;
bef0293 allow `evidences` to be passed directly as an arg (not only in `fields`) by deeenes <turei.denes@gmail.com> 2023-05-21 19:43:17 +0200;
ff22cd1 `unnest_evidences`: separate evidences by direction & effect, into new rows or columns by deeenes <turei.denes@gmail.com> 2023-05-21 19:28:45 +0200;
53bed6c arguments for `fromJSON` can be passed through any OmniPath downloading function by deeenes <turei.denes@gmail.com> 2023-05-21 19:25:48 +0200;
850ac30 log message about JSON column processing by deeenes <turei.denes@gmail.com> 2023-05-21 00:40:31 +0200;
446db29 deserialize upon download also the new `evidences` column by deeenes <turei.denes@gmail.com> 2023-05-21 00:31:56 +0200;
d834864 `deserialize_json_col`: convert extra_attrs, evidences, or any JSON column to lists by deeenes <turei.denes@gmail.com> 2023-05-21 00:30:28 +0200;
5835045 do not export non-functional `homology_translate` and `orthology_translate`; fixes <a href="#71">#71</a> by deeenes <turei.denes@gmail.com> 2023-05-15 14:27:10 +0200;
48f64ec Bump version: 3.9.1 → 3.9.2 by deeenes <turei.denes@gmail.com> 2023-05-04 05:01:43 +0200;
d58518e pkgdown site rebuild by deeenes <turei.denes@gmail.com> 2023-05-04 05:01:22 +0200;
91ab7ee connected OMA backend to orthology translation by deeenes <turei.denes@gmail.com> 2023-05-04 04:56:30 +0200;
f7c53f4 new built-in database definition: OMA orthologous pairs by deeenes <turei.denes@gmail.com> 2023-05-04 03:50:58 +0200;
6f5101b OMA: pairwise orthologous genes table by deeenes <turei.denes@gmail.com> 2023-05-04 03:35:57 +0200;
1914669 OMA ID types by deeenes <turei.denes@gmail.com> 2023-05-04 02:34:42 +0200;
ee5b5a4 `oma_code`: translate organisms to OMA codes by deeenes <turei.denes@gmail.com> 2023-05-04 01:48:15 +0200;