GitHub / LieberInstitute/spatialLIBD / commits
Code for the spatialLIBD R/Bioconductor package and shiny app
| SHA | Message | Author | Date | Stats |
|---|---|---|---|---|
| 2c4b4009 | Fix a fetch_data() link and bump version | Nick-Eagles <n****s@l****g> | about 1 month ago | |
| aeac846c | Document habenula atlas files and bump version after a fetch_data() fix | Nick-Eagles <n****s@l****g> | about 1 month ago | |
| f4beacfd | Fix a habenula atlas URL for fetch_data | Nick-Eagles <n****s@l****g> | about 1 month ago | |
| f6381931 | v1.25.3 -- uses scrapper + updated fetch_data() for habenulaAtlas project rel... | lcolladotor <l****r@g****m> | about 1 month ago | |
| 4486b3dc | Change dropbox link for sce_pb_visium_habenula_atlas.rds | lcolladotor <l****r@g****m> | about 1 month ago | |
| a4005a25 | merge Merge pull request #123 from LieberInstitute/scuttle_pseudobulk_check |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
about 1 month ago | |
| d410b054 | merge Merge branch 'devel' into scuttle_pseudobulk_check |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
about 1 month ago | |
| e3e22734 | Fix aggregateAcrossCells compatibility | manishabarse <m****d@g****m> | about 1 month ago | |
| 26e7f029 | Configure fetch_data() to load habenula atlas data | Nick-Eagles <n****s@l****g> | about 1 month ago | |
| a32ec183 | Prepare metadata for habenula atlas data | Nick-Eagles <n****s@l****g> | about 1 month ago | |
| 8d733724 | edit scuttle to scrapper for aggregateAcrossCells() | manishabarse <m****d@g****m> | about 1 month ago | |
| 94b68c69 | v1.25.2 -- fix colors on app at the layer-level tab | lcolladotor <l****r@g****m> | 4 months ago | |
| bf033c8f | Fix name of Xenium example in fetch_data() calls | lcolladotor <l****r@g****m> | 6 months ago | |
| 5f950950 | merge Merge pull request #121 from LieberInstitute/xenium_vis_functions |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
6 months ago | |
| 046bd0e4 | v1.25.1 -- `vis_*()` functions and `run_app()` now support visualizing Xenium... | lcolladotor <l****r@g****m> | 6 months ago | |
| 3d182105 | merge Merge remote-tracking branch 'upstream/devel' into xenium_vis_functions | lcolladotor <l****r@g****m> | 6 months ago | |
| 7d08e068 | Update fetch_data() for the spe_xenium_example data | lcolladotor <l****r@g****m> | 6 months ago | |
| ea237b0d | Add support on the shiny app for Xenium data | lcolladotor <l****r@g****m> | 6 months ago | |
| ed5d03a8 | Fix several things about the Xenium support in | lcolladotor <l****r@g****m> | 6 months ago | |
| f2750c57 | Make vis_grid_gene() and vis_grid_clus() support | lcolladotor <l****r@g****m> | 6 months ago | |
| 4ca4cb58 | vis_gene already inherits params from vis_clus | lcolladotor <l****r@g****m> | 6 months ago | |
| faff1678 | Update docs | lahuuki <l****i@g****m> | 6 months ago | |
| ed9c5f2b | get datatype arg in app_ui and app_server | lahuuki <l****i@g****m> | 6 months ago | |
| 4cdc7be0 | Add datatype checks | lahuuki <l****i@g****m> | 6 months ago | |
| 7d564032 | Add datatype as param to run_app - update docs | lahuuki <l****i@g****m> | 6 months ago | |
| 3f56fba4 | Fix Cross-refrences in descriptions | lahuuki <l****i@g****m> | 6 months ago | |
| dfb9a3c2 | fix spe_xenium_example name | lahuuki <l****i@g****m> | 6 months ago | |
| 3649ebf2 | Update date | lahuuki <l****i@g****m> | 6 months ago | |
| 4134d6a8 | Add xenium example, fix auto_crop | lahuuki <l****i@g****m> | 6 months ago | |
| 7d0ac111 | Adapt vis_gene for xenium data | lahuuki <l****i@g****m> | 6 months ago | |
| ab82404d | Fix typo | lahuuki <l****i@g****m> | 6 months ago | |
| 25cb967f | Add datatype arg to vis_gene | lahuuki <l****i@g****m> | 6 months ago | |
| 0823d989 | Update docs | lahuuki <l****i@g****m> | 6 months ago | |
| a4f21a32 | Add vis_gene_c | lahuuki <l****i@g****m> | 6 months ago | |
| 1a0206d2 | Bump date and version | lahuuki <l****i@g****m> | 6 months ago | |
| b84be4c3 | Fix typo in example | lahuuki <l****i@g****m> | 6 months ago | |
| 92b7ae59 | Fix cross link in docs (vis_gene_c not defined yet) | lahuuki <l****i@g****m> | 6 months ago | |
| 3587f094 | Update doc with fixed example | lahuuki <l****i@g****m> | 6 months ago | |
| 539787b8 | fix example, redefine d | lahuuki <l****i@g****m> | 6 months ago | |
| 3c879532 | fix unit | lahuuki <l****i@g****m> | 6 months ago | |
| 1b734e2f | use vis_clus_c for xenium datatype | lahuuki <l****i@g****m> | 6 months ago | |
| c981336f | Add xenium example | lahuuki <l****i@g****m> | 6 months ago | |
| 22392ae0 | clean up vis_clus_c example | lahuuki <l****i@g****m> | 6 months ago | |
| 2fed7895 | Add spe_xenium_example to fetch_data (need to update github when ready) | lahuuki <l****i@g****m> | 6 months ago | |
| 90d34881 | Add xenium example to experimenthub metadata for LFF ERC | lahuuki <l****i@g****m> | 6 months ago | |
| 4ac9bc9d | Update docs | lahuuki <l****i@g****m> | 6 months ago | |
| e534d9f2 | Update desciptions for vis_clus_*() functions | lahuuki <l****i@g****m> | 6 months ago | |
| b9dcff86 | Add vis_clus_c() function for handling visulization of Xenium/centroid based ... | lahuuki <l****i@g****m> | 6 months ago | |
| 42fcec07 | Add datatype param, check for correct input formats | lahuuki <l****i@g****m> | 6 months ago | |
| c9e01b22 | bump x.y.z version to even y prior to creation of RELEASE_3_23 branch | lshep <l****d@r****g> | 6 months ago | |
| 7026a931 | bump x.y.z version to odd y following creation of RELEASE_3_23 branch | lshep <l****d@r****g> | 6 months ago | |
| e4921b47 | Add top-level license for sponsor readiness | gpertea <g****a@g****m> | 8 months ago | |
| a5e8f899 | v1.23.2 -- accepted @lahuuki's PR #119. | lcolladotor <l****r@g****m> | 10 months ago | |
| 7471a769 | auto-reformat with air | lcolladotor <l****r@g****m> | 10 months ago | |
| f25a94cd | merge Merge pull request #119 from LieberInstitute/enrichment_list_genes |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
10 months ago | |
| 3e29ac31 | v1.23.1 -- fetch_data() now allows downloading LFF_spatial_ERC files thanks t... | lcolladotor <l****r@g****m> | 10 months ago | |
| 24a4d96b | Greatly expand the information about what publications to cite when using spa... | lcolladotor <l****r@g****m> | 10 months ago | |
| 84e78b24 | mostly auto-reformat code with air | lcolladotor <l****r@g****m> | 10 months ago | |
| 9712d1f5 | Switch to bioc version 3.21 | lcolladotor <l****r@g****m> | 10 months ago | |
| e3734364 | merge Merge pull request #118 from LieberInstitute/add_ERC_data |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
10 months ago | |
| 3445b31c | Add test for fetch_data(), confirm all dropbox links for ERC data | lahuuki <l****i@g****m> | 12 months ago | |
| 9f0cfde8 | Update docs | lahuuki <l****i@g****m> | 12 months ago | |
| 7188cf83 | Fix trailing comma | lahuuki <l****i@g****m> | 12 months ago | |
| 34f4b9b9 | Update fetch_data with ERC dropbox links | lahuuki <l****i@g****m> | 12 months ago | |
| 7d748065 | Move GeneList to last col | lahuuki <l****i@g****m> | 12 months ago | |
| 848f120d | Update metadata with corrected filenames | lahuuki <l****i@g****m> | 12 months ago | |
| 4b92cce6 | Add ERC 8 type opttions to fetch_data() | lahuuki <l****i@g****m> | 12 months ago | |
| 8c46036f | Fix ERC pseudobulk filenames | lahuuki <l****i@g****m> | 12 months ago | |
| 0dc6d32a | Add broad level pb and modeling data too | lahuuki <l****i@g****m> | 12 months ago | |
| 71393cde | Make metadata from scripts | lahuuki <l****i@g****m> | 12 months ago | |
| cfb09397 | Add metadata file for spatial ERC | lahuuki <l****i@g****m> | 12 months ago | |
| 20d2ef8c | bump x.y.z version to odd y following creation of RELEASE_3_22 branch | lshep <l****d@r****g> | about 1 year ago | |
| d06d43cd | bump x.y.z version to even y prior to creation of RELEASE_3_22 branch | lshep <l****d@r****g> | about 1 year ago | |
| b7bae6f5 | Change to use check suggested at https://blog.bioconductor.org/posts/2025-07-... | lcolladotor <l****r@g****m> | about 1 year ago | |
| 40da043d | v1.21.6 -- merged and close #115 | lcolladotor <l****r@g****m> | about 1 year ago | |
| f5a1ca75 | Fix some comments, from #115 | lcolladotor <l****r@g****m> | about 1 year ago | |
| 427a6215 | Auto-formatted code with Air | lcolladotor <l****r@g****m> | about 1 year ago | |
| 44d886a8 | Auto-formatted code with Air | lcolladotor <l****r@g****m> | about 1 year ago | |
| 2e260c46 | merge Merge pull request #115 from LieberInstitute/reg_pb_add_gene_search |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
about 1 year ago | |
| d547858f | Auto-reformatted some files with Air | lcolladotor <l****r@g****m> | about 1 year ago | |
| 91049719 | Fix this unit test now with ggplot2 v4.0.0 in mind | lcolladotor <l****r@g****m> | about 1 year ago | |
| 95dd3a1f | If gene_name and gene_id are in rowData, add gene_search as defined in check_... | lahuuki <l****i@g****m> | about 1 year ago | |
| aff00dbd | v1.21.5 -- depend on R 4.1 due to the use of the native R pipe | lcolladotor <l****r@g****m> | over 1 year ago | |
| 8c0fcd8f | v1.21.4 -- resolved a bug in registration_wrapper() noted by @manishabarse | lcolladotor <l****r@g****m> | over 1 year ago | |
| b8edaacb | merge Merge pull request #110 from LieberInstitute/fix_results_anova |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| b558b463 | Fix: return results_anova to registration_wrapper() | manishabarse <m****d@g****m> | over 1 year ago | |
| 3b5964f3 | v1.21.3 -- now registration_pseudobulk() is more compatible with scran::pseud... | lcolladotor <l****r@g****m> | over 1 year ago | |
| f904ae24 | Styling + add a mention about the length | lcolladotor <l****r@g****m> | over 1 year ago | |
| 224ff2a6 | merge Merge pull request #108 from LieberInstitute/pseudobulkDGE_compatable |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 36d54ecd | merge Merge branch 'devel' into pseudobulkDGE_compatable |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 1de57296 | v1.21.2 -- added vis_image() thanks to PR #107 by @lahuuki. | lcolladotor <l****r@g****m> | over 1 year ago | |
| 13b07ddd |
We don't need these lines
Co-authored-by: Nick Eagles <n****7@g****m> |
lcolladotor <l****r@g****m> | over 1 year ago | |
| 0678876a | merge Merge pull request #107 from LieberInstitute/add_vis_image_function |
Leonardo Collado-Torres <l****r@g****m>
Committed by: GitHub <n****y@g****m> |
over 1 year ago | |
| 9ba82481 | v1.21.1 -- resolve #106 by expanding the documentation of registration_pseudo... | lcolladotor <l****r@g****m> | over 1 year ago | |
| 0e32c655 | Add tests for pseudo qc vars | Louise Huuki <l****i@g****m> | over 1 year ago | |
| 39f8d15d | Add mito_gene var to calc pseudo_expr_mito | Louise Huuki <l****i@g****m> | over 1 year ago | |
| 7896bf6f | Add option to filter with edgeR::filterByExpr | Louise Huuki <l****i@g****m> | over 1 year ago | |
| fcb664cc | fix to sce_pseudo | Louise Huuki <l****i@g****m> | over 1 year ago | |
| a8593b68 | Fix example | Louise Huuki <l****i@g****m> | over 1 year ago | |
| 742b916d | Create new var_registration column in colData, this isolates changes to make ... | Louise Huuki <l****i@g****m> | over 1 year ago |