phenomix 0.99.6

New features

Transfer phenoRx::prepare_hpo to phenomix
Remove all ontology-related functions (now within HPOExplorer)
Explore bigstatsr/bigreadr a bit.
New functions, introduced while writing up thesis:
- clip_outliers
- run_cor
- run_knn_overlap
- un_ontological_similarity
- run_phate
- run_preseveration
- run_pseudotime_subtypes
- seurat_to_ontological_similarity

Bug fixes

Fix GH token in rworkflows yml

phenomix 0.99.5

New features

Add rworkflows
Offload element-extraction functions to scKirby
- extract_metadata -> get_obs
- extract_embeddings -> get_obsm
- extract_loadings -> get_varm
- extract_graph -> get_graphs
- extract_matrix -> get_x
- extract_colnames -> get_obs_names
- is_seurat -> is_class("seurat")
- is_matrix -> is_class("matrix")
extract_cor -> get_cor
gwas_matrix_magma -> magma_matrix
- Replace parallel with BiocParallel
Change args globally:
- reduction -> keys
- drop_MHC -> drop_mhc
Remove functions:
- create_DT
New functions:
- phenomix_query
- phenomix_matrix
- map_phenotypes
New data: OpenGWAS
- Supplied/prepared by opengwas_meta
Condense get_cs2g_ukb/get_cs2g_gwascatalog into get_cs2g.
Convert to using data.table
- Remove all reshape2 functions.
- Remove some dplyr functions.
New function: get_ctd

Bug fixes

Get rid of namespace conflicts: Warning messages:
- 1: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘phenomix’
- 2: replacing previous import ‘Matrix::head’ by ‘utils::head’ when loading ‘phenomix’

phenomix 0.99.4

New features

Added a NEWS.md file to track changes to the package.
Updated GHA, added Dockerfile, removed docs folder.

Bug fixes

gwas_matrix_magma: general improvements.