diff --git a/README.md b/README.md index f3926655..eb7dfd94 100644 --- a/README.md +++ b/README.md @@ -93,7 +93,7 @@ saved to `get_default_cache_dir()` unless a custom path is provided via the cache_directory argument. The `metadata` variable can then be re-used for all subsequent queries. -The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944). +The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607). The following sections demonstrate the metadata, quality control, generation of raw and normalised counts, and pseudobulk construction for @@ -231,7 +231,7 @@ Reading counts ■■■■■■■■■■■■■■■■■■■■■ single_cell_counts #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60 -#> # Features=33145 | Cells=2806 | Assays=counts +#> # [90mFeatures=33145 | Cells=2806 | Assays=counts[0m #> .cell observation_joinid dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA #> #> 1 80_1 zz-!e5_XAo 842c6f5d-4a94… 1de3f3ba… 1de3f3… "" 7fabaf1c-52fd-4… 14600 breast 1749 10.8 @@ -290,7 +290,7 @@ Reading cpm ■■■■■■■■■■■■■■■■■■■■■■ single_cell_cpm #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60 -#> # Features=33145 | Cells=2806 | Assays=cpm +#> # [90mFeatures=33145 | Cells=2806 | Assays=cpm[0m #> .cell observation_joinid dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA #> #> 1 80_1 zz-!e5_XAo 842c6f5d-4a94… 1de3f3ba… 1de3f3… "" 7fabaf1c-52fd-4… 14600 breast 1749 10.8 @@ -363,7 +363,7 @@ Reading sct ■■■■■■■■■■■■■■■■■■■■■■ single_cell_sct #> # A SingleCellExperiment-tibble abstraction: 1,193 × 60 -#> # Features=33145 | Cells=1193 | Assays=sct +#> # [90mFeatures=33145 | Cells=1193 | Assays=sct[0m #> .cell observation_joinid dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA #> #> 1 80_1 zz-!e5_XAo 842c6f5d-4a94… 1de3f3ba… 1de3f3… "" 7fabaf1c-52fd-4… 14600 breast 1749 10.8 @@ -418,7 +418,7 @@ Reading counts ■■■■■■■■■■■■■■■■■■■■■ pseudobulk_counts #> # A SingleCellExperiment-tibble abstraction: 139 × 43 -#> # Features=15888 | Cells=139 | Assays=counts +#> # [90mFeatures=15888 | Cells=139 | Assays=counts[0m #> .cell dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups cell_type_unified_en…¹ sample_chunk cell_chunk #> #> 1 2e8c9911c9bfbf… 0ba16f4b-… 2e8c9911… 2e8c99… "" HDBR15279,HDBR1… NA respiratory … cd14 mono 1 1 @@ -517,7 +517,7 @@ Reading cpm ■■■■■■■■■■■■■■■■■■■■■■ single_cell_cpm #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60 -#> # Features=1 | Cells=2806 | Assays=cpm +#> # [90mFeatures=1 | Cells=2806 | Assays=cpm[0m #> .cell observation_joinid dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA #> #> 1 80_1 zz-!e5_XAo 842c6f5d-4a94… 1de3f3ba… 1de3f3… "" 7fabaf1c-52fd-4… 14600 breast 1749 10.8 @@ -813,7 +813,7 @@ get_metadata( #> ℹ Reading files. #> ℹ Compiling Experiment. #> # A SingleCellExperiment-tibble abstraction: 500 × 7 -#> # Features=13132 | Cells=500 | Assays=counts +#> # [90mFeatures=13132 | Cells=500 | Assays=counts[0m #> .cell sample_id dataset_id cell_type_unified_ensemble atlas_id file_id_cellNexus_single_cell original_cell_ #> #> 1 AAACATACAACCAC_1 pbmc3k pbmc3k Memory CD4 T cellxgene/03-10-2025 67e196a3c4e145151fc9e06c200e2f7f.h5ad AAACATACAACCAC diff --git a/index.md b/index.md index c2e00dd7..2f7f0839 100644 --- a/index.md +++ b/index.md @@ -61,7 +61,7 @@ The QC flags used throughout `cellNexus` are computed on sample-level using [HPC ## Metadata Explore -Through harmonisation and curation, `cellNexus` adds columns that are not present in the original CELLxGENE metadata alone. +Through harmonisation and curation, `cellNexus` adds columns that are not present in the original CELLxGENE metadata alone. The latest metadata is downloaded automatically when you call `get_metadata()` — no need to supply a download link manually. See the client usage examples for details on the columns available. | Column | Description | |--------|-------------| diff --git a/vignettes/cellNexus.Rmd b/vignettes/cellNexus.Rmd index 5bcb1579..136a7f90 100644 --- a/vignettes/cellNexus.Rmd +++ b/vignettes/cellNexus.Rmd @@ -84,7 +84,7 @@ suppressPackageStartupMessages({ ### Load the metadata By default, `get_metadata()` loads harmonised annotations. Metadata is saved to `get_default_cache_dir()` unless a custom path is provided via the cache_directory argument. The `metadata` variable can then be re-used for all subsequent queries. -The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944). +The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607). The following sections demonstrate the metadata, quality control, generation of raw and normalised counts, and pseudobulk construction for the specified query. @@ -220,7 +220,7 @@ Reading counts â– â– â– â– â– â– â– â– â– â single_cell_counts #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60 -#> # Features=33145 | Cells=2806 | Assays=counts +#> # [90mFeatures=33145 | Cells=2806 | Assays=counts[0m #> .cell observation_joinid dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA #> #> 1 80_1 zz-!e5_XAo 842c6f5d-4a94… 1de3f3ba… 1de3f3… "" 7fabaf1c-52fd-4… 14600 breast 1749 10.8 @@ -280,7 +280,7 @@ Reading cpm â– â– â– â– â– â– â– â– â– â– single_cell_cpm #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60 -#> # Features=33145 | Cells=2806 | Assays=cpm +#> # [90mFeatures=33145 | Cells=2806 | Assays=cpm[0m #> .cell observation_joinid dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA #> #> 1 80_1 zz-!e5_XAo 842c6f5d-4a94… 1de3f3ba… 1de3f3… "" 7fabaf1c-52fd-4… 14600 breast 1749 10.8 @@ -353,7 +353,7 @@ Reading sct â– â– â– â– â– â– â– â– â– â– single_cell_sct #> # A SingleCellExperiment-tibble abstraction: 1,193 × 60 -#> # Features=33145 | Cells=1193 | Assays=sct +#> # [90mFeatures=33145 | Cells=1193 | Assays=sct[0m #> .cell observation_joinid dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA #> #> 1 80_1 zz-!e5_XAo 842c6f5d-4a94… 1de3f3ba… 1de3f3… "" 7fabaf1c-52fd-4… 14600 breast 1749 10.8 @@ -408,7 +408,7 @@ Reading counts â– â– â– â– â– â– â– â– â– â pseudobulk_counts #> # A SingleCellExperiment-tibble abstraction: 139 × 43 -#> # Features=15888 | Cells=139 | Assays=counts +#> # [90mFeatures=15888 | Cells=139 | Assays=counts[0m #> .cell dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups cell_type_unified_en…¹ sample_chunk cell_chunk #> #> 1 2e8c9911c9bfbf… 0ba16f4b-… 2e8c9911… 2e8c99… "" HDBR15279,HDBR1… NA respiratory … cd14 mono 1 1 @@ -497,7 +497,7 @@ Reading cpm â– â– â– â– â– â– â– â– â– â– single_cell_cpm #> # A SingleCellExperiment-tibble abstraction: 2,806 × 60 -#> # Features=1 | Cells=2806 | Assays=cpm +#> # [90mFeatures=1 | Cells=2806 | Assays=cpm[0m #> .cell observation_joinid dataset_id sample_id sample_ experiment___ run_from_cell_id sample_heuristic age_days tissue_groups nFeature_expressed_i…¹ nCount_RNA #> #> 1 80_1 zz-!e5_XAo 842c6f5d-4a94… 1de3f3ba… 1de3f3… "" 7fabaf1c-52fd-4… 14600 breast 1749 10.8 @@ -769,7 +769,7 @@ get_metadata( #> ℹ Reading files. #> ℹ Compiling Experiment. #> # A SingleCellExperiment-tibble abstraction: 500 × 7 -#> # Features=13132 | Cells=500 | Assays=counts +#> # [90mFeatures=13132 | Cells=500 | Assays=counts[0m #> .cell sample_id dataset_id cell_type_unified_ensemble atlas_id file_id_cellNexus_single_cell original_cell_ #> #> 1 AAACATACAACCAC_1 pbmc3k pbmc3k Memory CD4 T cellxgene/03-10-2025 67e196a3c4e145151fc9e06c200e2f7f.h5ad AAACATACAACCAC diff --git a/vignettes/cellNexus.Rmd.orig b/vignettes/cellNexus.Rmd.orig index af1d5074..2f5c7e66 100644 --- a/vignettes/cellNexus.Rmd.orig +++ b/vignettes/cellNexus.Rmd.orig @@ -83,7 +83,7 @@ suppressPackageStartupMessages({ ### Load the metadata By default, `get_metadata()` loads harmonised annotations. Metadata is saved to `get_default_cache_dir()` unless a custom path is provided via the cache_directory argument. The `metadata` variable can then be re-used for all subsequent queries. -The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944). +The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607). The following sections demonstrate the metadata, quality control, generation of raw and normalised counts, and pseudobulk construction for the specified query. diff --git a/vignettes/gene-expression-explore.Rmd b/vignettes/gene-expression-explore.Rmd index b2115677..a5108ead 100644 --- a/vignettes/gene-expression-explore.Rmd +++ b/vignettes/gene-expression-explore.Rmd @@ -11,7 +11,7 @@ vignette: > # Overview -The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944). +The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607). This page focuses on expression-layer retrieval workflows after metadata filtering. diff --git a/vignettes/gene-expression-explore.Rmd.orig b/vignettes/gene-expression-explore.Rmd.orig index 18876c1c..c813036a 100644 --- a/vignettes/gene-expression-explore.Rmd.orig +++ b/vignettes/gene-expression-explore.Rmd.orig @@ -13,7 +13,7 @@ knitr::opts_chunk$set(collapse = TRUE, comment = "#>") # Overview -The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21388944/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21388944](https://zenodo.org/records/21388944). +The unified pseudobulk AnnData object was pre-generated outside of this vignette applying quality control and retaining at least 15,000 intersecting genes across samples and hosted on Zenodo to avoid lengthy recompilation. Download the latest version: [pseudobulk_se.h5ad](https://zenodo.org/records/21633607/files/pseudobulk_se.h5ad?download=1). For all versions: [10.5281/zenodo.21633607](https://zenodo.org/records/21633607). This page focuses on expression-layer retrieval workflows after metadata filtering.