diff --git a/pr-preview/pr-344/_sources/trajectories/pseudotemporal.ipynb b/pr-preview/pr-344/_sources/trajectories/pseudotemporal.ipynb index 59d7fcef..2e602e23 100644 --- a/pr-preview/pr-344/_sources/trajectories/pseudotemporal.ipynb +++ b/pr-preview/pr-344/_sources/trajectories/pseudotemporal.ipynb @@ -45,7 +45,7 @@ "`````\n", "``````\n", "\n", - "````{dropdown} Access to data and notebook\n", + "````{dropdown}    Access to data and notebook\n", "```{include} ../_static/default_text_lamindb_setup.md\n", "```\n", "````" diff --git a/pr-preview/pr-344/_static/default_text_lamindb_setup.md b/pr-preview/pr-344/_static/default_text_lamindb_setup.md index ce9498d5..0edd24e3 100644 --- a/pr-preview/pr-344/_static/default_text_lamindb_setup.md +++ b/pr-preview/pr-344/_static/default_text_lamindb_setup.md @@ -41,11 +41,12 @@ We acknowledge free hosting from [Lamin Labs](https://lamin.ai/). ```python import lamindb as ln - af = ln.Artifact.get(key="key_of_dataset", is_latest=True) + af = ln.Artifact.get(key="key_of_dataset", is_latest=True) # or ln.Artifact("SOMEID").get() obj = af.load() ``` The object is now accessible in memory and is ready for analysis. + Adapt the `ln.Artifact("SOMEID").get()` suffix to get older versions like `ln.Artifact("SOMEID0001").get()` to get the second uploaded version. 6. **Accessing notebooks (Transforms)** @@ -57,7 +58,8 @@ We acknowledge free hosting from [Lamin Labs](https://lamin.ai/). ``` which will download the notebook to the current working directory. + Analogously to `Artifacts`, you can adapt the suffix ID to get older versions. -7. \*\*On `ln.track()` and `ln.finish()` +7. **On `ln.track()` and `ln.finish()`** - These functions are currently only available for users with write access and may error. Please comment them out for now. diff --git a/pr-preview/pr-344/searchindex.js b/pr-preview/pr-344/searchindex.js index a370c8ef..aeafdbb5 100644 --- a/pr-preview/pr-344/searchindex.js +++ b/pr-preview/pr-344/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"A Note on UMI Errors": [[23, null]], "A brief history of sequencing": [[24, "a-brief-history-of-sequencing"]], "A more mathematical description of deconvolution": [[36, "a-more-mathematical-description-of-deconvolution"]], "A note on alignment orientation": [[23, null]], "A note on preceding steps": [[23, null]], "A note on scalability": [[7, null]], "A note on sequencing length": [[24, null]], "A note on the redundancy between gene sets and the performance of preranked and fry gene set tests": [[15, "a-note-on-the-redundancy-between-gene-sets-and-the-performance-of-preranked-and-fry-gene-set-tests"]], "A real-world example": [[23, "a-real-world-example"]], "ADT": [[12, "adt"]], "AIR analysis on RNA clusters": [[3, "air-analysis-on-rna-clusters"]], "AIR repertoire analysis": [[2, "air-repertoire-analysis"]], "API overview": [[19, "api-overview"]], "ATAC": [[12, "atac"]], "Accessing Python from R": [[21, "accessing-python-from-r"]], "Accessing R from Python": [[21, "accessing-r-from-python"]], "Acknowledgements": [[0, null]], "Adding aligned metadata": [[19, "adding-aligned-metadata"]], "Advanced integration": [[27, null]], "Advanced: Multimodal data analysis with muon": [[19, "advanced-multimodal-data-analysis-with-muon"]], "Advanced: Using MuData to store multimodal data": [[19, "advanced-using-mudata-to-store-multimodal-data"]], "Alignment and mapping": [[23, "alignment-and-mapping"]], "Alternative formats": [[30, "alternative-formats"]], "Analysing single-pooled CRISPR screens": [[16, "analysing-single-pooled-crispr-screens"]], "Analysis frameworks and tools": [[19, null]], "Analytic Pearson residuals": [[33, "analytic-pearson-residuals"]], "Annotation": [[5, null], [43, null]], "Annotation by mapping to a reference": [[5, "annotation-by-mapping-to-a-reference"]], "Approaches": [[17, "approaches"], [25, "approaches"]], "Assigning AIR State": [[2, "assigning-air-state"]], "Assumptions & Limitations": [[25, "assumptions-limitations"]], "Atlas building and reference mapping": [[29, "atlas-building-and-reference-mapping"]], "Augur model": [[16, null]], "Authors": [[5, "authors"], [6, "authors"], [7, "authors"], [8, "authors"], [9, "authors"], [11, "authors"], [13, "authors"], [14, "authors"], [15, "authors"], [16, "authors"], [17, "authors"], [19, "authors"], [21, "authors"], [23, "authors"], [24, "authors"], [26, "authors"], [27, "authors"], [28, "authors"], [31, "authors"], [32, "authors"], [33, "authors"], [34, "authors"], [36, "authors"], [37, "authors"], [38, "authors"], [39, "authors"], [40, "authors"], [41, "authors"], [43, "authors"], [44, "authors"], [45, "authors"], [46, "authors"], [47, "authors"], [48, "authors"], [49, "authors"], [50, "authors"]], "Authors:": [[25, "authors"]], "Automated annotation": [[5, "automated-annotation"], [43, "automated-annotation"]], "BCR Data Analysis with Dandelion": [[1, "bcr-data-analysis-with-dandelion"]], "BCR specificity analysis": [[4, "bcr-specificity-analysis"]], "Background": [[17, "background"]], "Batch correction": [[44, null]], "Batch removal complexity": [[7, "batch-removal-complexity"]], "Batch-aware feature selection": [[7, "batch-aware-feature-selection"]], "Benchmarking": [[29, "benchmarking"]], "Benchmarking your own integration": [[7, "benchmarking-your-own-integration"]], "Benisse": [[3, "benisse"]], "Bioconductor": [[21, "bioconductor"]], "Bioconductor OSCA and OSTA books": [[22, "bioconductor-osca-and-osta-books"]], "Brief discussion": [[23, "brief-discussion"]], "Building the index": [[23, "building-the-index"]], "Building the model": [[7, "building-the-model"]], "Building the reference": [[27, "building-the-reference"]], "Bulk deconvolution": [[17, null]], "CITE-seq data": [[28, "cite-seq-data"]], "Calculate a batch-corrected UMAP": [[7, "calculate-a-batch-corrected-umap"]], "Calculate and visualize tumors\u2019 statistics": [[49, "calculate-and-visualize-tumors-statistics"]], "Calculating QC metrics": [[11, "calculating-qc-metrics"]], "Calculating local perturbation signatures": [[16, "calculating-local-perturbation-signatures"]], "Case Study": [[25, "case-study"]], "Case study: Pathway enrichment analysis and activity level scoring in human PBMC single cells": [[15, "case-study-pathway-enrichment-analysis-and-activity-level-scoring-in-human-pbmc-single-cells"]], "Cassiopeia for lineage tracing analysis": [[49, "cassiopeia-for-lineage-tracing-analysis"]], "Cell barcode correction": [[23, "cell-barcode-correction"]], "Cell isolation": [[2, "cell-isolation"]], "Cell-Aligned Data": [[2, "cell-aligned-data"]], "Cell-cell communication": [[25, null]], "Cell-level pathway activity scoring using AUCell": [[15, "cell-level-pathway-activity-scoring-using-aucell"]], "Cell-type specific expression of every gene in the spatial data": [[36, "cell-type-specific-expression-of-every-gene-in-the-spatial-data"]], "Cell2Location cell type mapping": [[36, "cell2location-cell-type-mapping"]], "Cell2Location in practice": [[36, "cell2location-in-practice"]], "Cell2location": [[36, "cell2location"]], "Centered Log-Ratio normalization": [[47, "centered-log-ratio-normalization"]], "Choosing an integration method": [[7, "choosing-an-integration-method"]], "Citation": [[30, "citation"]], "Classifiers based on a wider set of genes": [[5, "classifiers-based-on-a-wider-set-of-genes"]], "Clonal expansion": [[1, "clonal-expansion"]], "Clonal expansion: diversity and abundance": [[1, "clonal-expansion-diversity-and-abundance"]], "Clonotype abundance": [[1, "clonotype-abundance"]], "Clonotype analysis": [[1, null]], "Clonotype definition": [[1, "clonotype-definition"], [1, "id13"]], "Cluster-level gene set enrichment analysis with decoupler": [[15, "cluster-level-gene-set-enrichment-analysis-with-decoupler"]], "Clustering": [[6, null]], "Clustering human bone marrow cells": [[6, "clustering-human-bone-marrow-cells"]], "Co-occurrence across spatial dimensions": [[40, "co-occurrence-across-spatial-dimensions"]], "CoNGA": [[3, "conga"]], "Collecting cellranger outputs into MuData object": [[48, "collecting-cellranger-outputs-into-mudata-object"]], "Combining NicheNet output with ligand-receptor inference": [[25, "combining-nichenet-output-with-ligand-receptor-inference"]], "Common gene set between reference and spatial dataset": [[38, "common-gene-set-between-reference-and-spatial-dataset"]], "Common observations": [[19, "common-observations"]], "Comparisons of data integration methods": [[7, "comparisons-of-data-integration-methods"]], "Compositional analysis": [[13, null]], "Computational tools to interpret time-course lineage tracing data": [[49, "computational-tools-to-interpret-time-course-lineage-tracing-data"]], "Computing the map from single-cells to spatial voxels": [[38, "computing-the-map-from-single-cells-to-spatial-voxels"]], "Conclusions": [[49, "conclusions"]], "Configure data": [[27, "configure-data"]], "Constructing a map between technologies": [[38, "constructing-a-map-between-technologies"]], "Contact us": [[30, "contact-us"]], "Contributing": [[30, "contributing"]], "Contributions": [[25, "contributions"]], "Contributors": [[5, "contributors"], [6, "contributors"], [7, "contributors"], [8, "contributors"], [9, "contributors"], [11, "contributors"], [13, "contributors"], [14, "contributors"], [15, "contributors"], [16, "contributors"], [17, "contributors"], [19, "contributors"], [21, "contributors"], [23, "contributors"], [24, "contributors"], [26, "contributors"], [27, "contributors"], [28, "contributors"], [31, "contributors"], [32, "contributors"], [33, "contributors"], [34, "contributors"], [36, "contributors"], [37, "contributors"], [38, "contributors"], [39, "contributors"], [40, "contributors"], [41, "contributors"], [43, "contributors"], [44, "contributors"], [45, "contributors"], [46, "contributors"], [47, "contributors"], [48, "contributors"], [49, "contributors"], [50, "contributors"]], "Conversion of muon objects to Seurat objects to use in downstream analysis": [[10, null]], "Conversion to DataFrames": [[19, "conversion-to-dataframes"]], "Convert Seurat assay to chromatin assay": [[10, "convert-seurat-assay-to-chromatin-assay"]], "Correction of ambient RNA": [[34, "correction-of-ambient-rna"]], "Count cells in neighbourhoods": [[13, "count-cells-in-neighbourhoods"]], "Count data representation": [[23, "count-data-representation"]], "Count distribution-based doublet scoring": [[11, "count-distribution-based-doublet-scoring"]], "Count matrix quality control": [[23, "count-matrix-quality-control"]], "Coverage-based doublet scoring": [[11, "coverage-based-doublet-scoring"]], "Create pseudo-bulk samples and explore the data": [[15, "create-pseudo-bulk-samples-and-explore-the-data"]], "Current best practices in single-cell RNA-seq analysis: a tutorial": [[22, "current-best-practices-in-single-cell-rna-seq-analysis-a-tutorial"]], "Curse of dimensionality": [[31, null]], "DSB normalization": [[47, "dsb-normalization"]], "Dandelion interoperability": [[1, "dandelion-interoperability"]], "Data Preparation": [[3, "data-preparation"], [3, "id7"]], "Data Preprocessing": [[3, "data-preprocessing"]], "Data characteristics - feature definition and sparsity": [[9, "data-characteristics-feature-definition-and-sparsity"]], "Data exploration": [[16, "data-exploration"]], "Data infrastructure": [[20, null]], "Data integration": [[7, null]], "Data loading": [[13, "data-loading"], [50, "data-loading"], [51, "data-loading"]], "Data normalization": [[15, "data-normalization"]], "Data preparation": [[7, "data-preparation"]], "Data preprocessing": [[17, "data-preprocessing"], [51, "data-preprocessing"]], "Database Preparation": [[4, "database-preparation"]], "Database Queries": [[4, "database-queries"], [4, "id13"]], "Database query via distance metrics": [[4, "database-query-via-distance-metrics"]], "Dataset": [[2, "dataset"], [7, "dataset"], [11, "dataset"]], "Dataset description": [[26, "dataset-description"]], "Deconvolving bulk COVID-19 whole blood samples": [[17, "deconvolving-bulk-covid-19-whole-blood-samples"]], "Deconvolving using MuSiC": [[17, "deconvolving-using-music"]], "Define neighbourhoods": [[13, "define-neighbourhoods"]], "Determining the most important genes for the prioritization": [[16, "determining-the-most-important-genes-for-the-prioritization"]], "Differential gene expression analysis": [[14, null]], "Differential prioritization": [[16, "differential-prioritization"]], "Dimensionality Reduction": [[31, null], [45, null]], "Discrete tissue regions": [[36, "discrete-tissue-regions"]], "Disk-based interoperability": [[21, "disk-based-interoperability"]], "Distance Measurements": [[4, "distance-measurements"]], "Distances": [[4, "distances"]], "Doublet Detection": [[34, "doublet-detection"]], "Doublet detection": [[11, "doublet-detection"], [23, "doublet-detection"], [46, null]], "Doublets detected with cell type markers": [[46, "doublets-detected-with-cell-type-markers"]], "Down-stream tasks and outlook": [[50, "down-stream-tasks-and-outlook"]], "Downloading the data": [[49, "downloading-the-data"]], "Downstream analysis": [[36, "downstream-analysis"]], "Early stopping": [[7, null]], "Efficient data access": [[19, "efficient-data-access"]], "Empty droplet detection": [[23, "empty-droplet-detection"]], "End-to-end pipelines": [[29, "end-to-end-pipelines"]], "Environment setup": [[5, "environment-setup"], [10, "environment-setup"], [14, "environment-setup"], [17, "environment-setup"], [25, "environment-setup"], [26, "environment-setup"], [27, "environment-setup"], [28, "environment-setup"], [44, "environment-setup"], [45, "environment-setup"], [46, "environment-setup"], [47, "environment-setup"], [50, "environment-setup"], [51, "environment-setup"]], "Environment setup and data": [[34, "environment-setup-and-data"], [37, "environment-setup-and-data"], [40, "environment-setup-and-data"], [41, "environment-setup-and-data"], [48, "environment-setup-and-data"]], "Environment setup.": [[49, "environment-setup"]], "Epitope Prediction": [[4, "epitope-prediction"]], "Evaluating the predicted IFN-\u03b2 response": [[16, "evaluating-the-predicted-ifn-response"]], "Examine the data": [[49, "examine-the-data"]], "Executing CoNGA": [[3, "executing-conga"]], "Experimental assay": [[9, "experimental-assay"]], "Extracting the embedding": [[7, "extracting-the-embedding"]], "Feature selection": [[32, null]], "FigR": [[8, "figr"]], "Filtering": [[2, "filtering"]], "Filtering cells": [[11, "filtering-cells"]], "Filtering features": [[11, "filtering-features"]], "Filtering low quality cells": [[34, "filtering-low-quality-cells"]], "Filtering out low-quality tumors": [[49, "filtering-out-low-quality-tumors"]], "Filtering out the gene sets with low number of genes": [[15, "filtering-out-the-gene-sets-with-low-number-of-genes"]], "First-generation sequencing": [[24, "first-generation-sequencing"]], "Fitting the reference model": [[36, "fitting-the-reference-model"]], "Fluidigm C1": [[24, "fluidigm-c1"]], "Formation of adaptive immune receptors by V(D)J recombination": [[2, "formation-of-adaptive-immune-receptors-by-v-d-j-recombination"]], "From cluster differentially expressed genes to cluster annotation": [[5, "from-cluster-differentially-expressed-genes-to-cluster-annotation"]], "From markers to cluster annotation": [[5, "from-markers-to-cluster-annotation"]], "Further Models in Reference Based Deconvolution": [[36, "further-models-in-reference-based-deconvolution"]], "GEX analysis on AIR clusters": [[3, "gex-analysis-on-air-clusters"]], "Gamma-Poisson distribution": [[33, null]], "Gathering TF regulons from public data": [[26, "gathering-tf-regulons-from-public-data"]], "Gene regulatory network inference using RNA and ATAC features": [[8, "gene-regulatory-network-inference-using-rna-and-atac-features"]], "Gene regulatory networks": [[26, null]], "Gene regulatory networks using chromatin accessibility": [[8, null]], "Gene segment usage": [[1, "gene-segment-usage"]], "Gene segment usage and spectratype": [[1, "gene-segment-usage-and-spectratype"]], "Gene set enrichment and pathway analysis": [[15, null]], "Gene set enrichment for complex experimental designs using limma-fry and pseudo-bulks": [[15, "gene-set-enrichment-for-complex-experimental-designs-using-limma-fry-and-pseudo-bulks"]], "Gene set test vs. pathway activity inference": [[15, "gene-set-test-vs-pathway-activity-inference"]], "Gene set tests and pathway analysis": [[15, "gene-set-tests-and-pathway-analysis"]], "Gene usage": [[1, "gene-usage"]], "General remarks": [[5, "general-remarks"]], "General settings": [[51, "general-settings"]], "Generating a Ligand-Receptor consensus with LIANA": [[25, "generating-a-ligand-receptor-consensus-with-liana"]], "Generation of GRNs using RNA data": [[26, "generation-of-grns-using-rna-data"]], "Glossary": [[18, null]], "Graph construction": [[27, "graph-construction"]], "Graph-based integration": [[7, "graph-based-integration"]], "H5AD": [[21, "h5ad"]], "HDF5-based formats": [[21, "hdf5-based-formats"]], "Harmony": [[44, "harmony"]], "How many genes to use?": [[7, null]], "Hyperparameters of SpaGCN": [[37, "hyperparameters-of-spagcn"]], "IRs of the adaptive immune system": [[2, "irs-of-the-adaptive-immune-system"]], "Identical matches": [[4, "identical-matches"]], "Identifying cells with no detectable perturbation": [[16, "identifying-cells-with-no-detectable-perturbation"]], "Identifying interactions between spatial communities": [[40, "identifying-interactions-between-spatial-communities"]], "Identifying the cell types most affected by perturbations": [[16, "conditions-perturbation-modeling-key-takeaway-1"]], "Immune Receptor Profiling": [[2, null]], "Immune receptor sequencing": [[2, "immune-receptor-sequencing"]], "Imputation": [[38, null]], "Imputing genes and mapping cell-types to space": [[38, "imputing-genes-and-mapping-cell-types-to-space"]], "In-memory interoperability": [[21, "in-memory-interoperability"]], "Inferring expansion events": [[49, "inferring-expansion-events"]], "Inferring pseudotime for adult human bone marrow": [[50, "inferring-pseudotime-for-adult-human-bone-marrow"]], "Inferring tree plasticity": [[49, "inferring-tree-plasticity"]], "Initializing a MuData object": [[19, "initializing-a-mudata-object"]], "Initializing an AnnData object": [[19, "initializing-an-anndata-object"]], "Inspecting quality control metrics": [[31, "inspecting-quality-control-metrics"]], "Install and load FigR package": [[8, "install-and-load-figr-package"]], "Installation": [[19, "installation"], [19, "id12"], [19, "id18"], [19, "id20"]], "Integrate gene expression and histology into a Graph": [[37, "integrate-gene-expression-and-histology-into-a-graph"]], "Integrating AIR and transcriptomics": [[3, null]], "Integrating BCR and GEX": [[3, "integrating-bcr-and-gex"]], "Integrating TCR and GEX": [[3, "integrating-tcr-and-gex"]], "Integrating UMI and full-length data": [[7, null]], "Integration with partially overlapping data and query-to-reference mapping with totalVI": [[27, "integration-with-partially-overlapping-data-and-query-to-reference-mapping-with-totalvi"]], "Interoperability": [[21, null]], "Interoperability between R ecosystems": [[21, "interoperability-between-r-ecosystems"]], "Interoperability for multimodal data": [[21, "interoperability-for-multimodal-data"]], "Interoperability with other languages": [[21, "interoperability-with-other-languages"]], "Interpretation of results": [[26, "interpretation-of-results"]], "Introduction": [[4, "introduction"], [30, "introduction"]], "JavaScript": [[21, "javascript"]], "Julia": [[21, "julia"]], "Key takeaways": [[25, "key-takeaways"], [49, "key-takeaways"]], "Label harmonization": [[7, null]], "Layers": [[19, "layers"]], "License": [[30, "license"]], "Ligand-receptor inference": [[25, "ligand-receptor-inference"]], "Limitations and traps": [[17, "limitations-and-traps"]], "Limitations of Augur": [[16, "limitations-of-augur"]], "Limitations of TF regulons": [[26, "limitations-of-tf-regulons"]], "Lineage tracing": [[49, null]], "Lineage tracing technologies": [[49, "lineage-tracing-technologies"]], "Linear embedding integration using Mutual Nearest Neighbors (MNN)": [[7, "linear-embedding-integration-using-mutual-nearest-neighbors-mnn"]], "Load NicheNet Prior-Knowledge": [[25, "load-nichenet-prior-knowledge"]], "Load data": [[2, "load-data"], [5, "load-data"], [10, "load-data"]], "Loading Data": [[17, "loading-data"]], "Loading R": [[17, "loading-r"]], "Loading the complete MuData object": [[48, "loading-the-complete-mudata-object"]], "Loading the data": [[44, "loading-the-data"], [45, "loading-the-data"], [46, "loading-the-data"], [47, "loading-the-data"]], "Loom": [[21, "loom"]], "Lower bound QC thresholds": [[11, "lower-bound-qc-thresholds"]], "Manual Query": [[4, "manual-query"]], "Manual annotation": [[5, "manual-annotation"], [43, "manual-annotation"]], "Mapping ADT onto an RNA atlas with bridge integration": [[27, "mapping-adt-onto-an-rna-atlas-with-bridge-integration"]], "Mapping against different reference sequences": [[23, "mapping-against-different-reference-sequences"]], "Mapping and quantification": [[23, "mapping-and-quantification"]], "Mapping to an augmented transcriptome": [[23, "mapping-to-an-augmented-transcriptome"]], "Mapping to the full genome": [[23, "mapping-to-the-full-genome"]], "Mapping to the spliced transcriptome": [[23, "mapping-to-the-spliced-transcriptome"]], "Marker gene-based classifiers": [[5, "marker-gene-based-classifiers"]], "Markers for cluster annotations across modalities": [[12, null]], "Microfluidic device-based protocols": [[24, "microfluidic-device-based-protocols"]], "Modality prediction": [[29, "modality-prediction"]], "Model construction and training": [[16, "model-construction-and-training"]], "Modeling RNA velocity": [[51, "modeling-rna-velocity"]], "Modelling differential intercellular signalling with NicheNet": [[25, "modelling-differential-intercellular-signalling-with-nichenet"]], "Moran\u2019s I score in Squidpy": [[41, "moran-s-i-score-in-squidpy"]], "Motif sequence analysis": [[1, "motif-sequence-analysis"], [1, "id23"]], "Motivation": [[3, "motivation"], [5, "motivation"], [6, "motivation"], [7, "motivation"], [8, "motivation"], [9, "motivation"], [11, "motivation"], [13, "motivation"], [14, "motivation"], [15, "motivation"], [16, "motivation"], [16, "id10"], [21, "motivation"], [23, "motivation"], [25, "motivation"], [26, "motivation"], [27, "motivation"], [28, "motivation"], [32, "motivation"], [33, "motivation"], [34, "motivation"], [36, "motivation"], [37, "motivation"], [38, "motivation"], [39, "motivation"], [40, "motivation"], [41, "motivation"], [43, "motivation"], [44, "motivation"], [45, "motivation"], [46, "motivation"], [47, "motivation"], [48, "motivation"], [49, "motivation"], [50, "motivation"], [51, "motivation"]], "MuData attributes": [[19, "mudata-attributes"]], "MuData views": [[19, "mudata-views"]], "Multi-Omics Factor Analysis (MOFA+)": [[28, "multi-omics-factor-analysis-mofa"]], "Multi-cell resolution": [[39, "multi-cell-resolution"]], "MultiVI": [[28, "multivi"]], "Multimodal Integration": [[3, "multimodal-integration"]], "Multimodal methods": [[19, "multimodal-methods"]], "Multiome data": [[28, "multiome-data"]], "Multiple groups": [[14, "multiple-groups"]], "Nanopore single-cell transcriptome sequencing": [[24, "nanopore-single-cell-transcriptome-sequencing"]], "Neighborhood analysis": [[40, null]], "New directions": [[17, "new-directions"], [49, "new-directions"], [51, "new-directions"]], "New on-disk formats": [[21, "new-on-disk-formats"]], "New phylogenetic inference algorithms": [[49, "new-phylogenetic-inference-algorithms"]], "Nomenclature": [[21, "nomenclature"]], "Normalization": [[33, null], [47, null]], "Note on using an Apple silicon-based device": [[23, null]], "Notes on edgeR": [[14, "notes-on-edger"]], "Nucleosome signal": [[11, "nucleosome-signal"]], "Null hypotheses in gene set enrichment analysis": [[15, "null-hypotheses-in-gene-set-enrichment-analysis"]], "Number of intBCs per Tumor": [[49, "number-of-intbcs-per-tumor"]], "Observation/variable-level matrices": [[19, "observation-variable-level-matrices"]], "Observational or Variable level": [[19, "observational-or-variable-level"]], "On the effect of filtering low-expression genes": [[15, "on-the-effect-of-filtering-low-expression-genes"]], "One group": [[14, "one-group"], [14, "id21"]], "Outcome of the analysis": [[26, "outcome-of-the-analysis"]], "Outlook": [[29, null]], "Output": [[3, "output"], [3, 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Acknowledgements", "39. Clonotype analysis", "38. Immune Receptor Profiling", "44. Integrating AIR and transcriptomics", "43. Specificity analysis", "11. Annotation", "10. Clustering", "12. Data integration", "25. Gene regulatory networks using chromatin accessibility", "23. Single-cell ATAC sequencing", "Conversion of muon objects to Seurat objects to use in downstream analysis", "24. Quality Control", "Markers for cluster annotations across modalities", "17. Compositional analysis", "16. Differential gene expression analysis", "18. Gene set enrichment and pathway analysis", "19. Perturbation modeling", "22. Bulk deconvolution", "50. Glossary", "4. Analysis frameworks and tools", "Data infrastructure", "5. Interoperability", "1. Prior art", "3. Raw data processing", "2. Single-cell RNA sequencing", "21. Cell-cell communication", "20. Gene regulatory networks", "46. Advanced integration", "45. Paired integration", "48. Outlook", "Single-cell best practices", "9. 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"a-note-on-the-redundancy-between-gene-sets-and-the-performance-of-preranked-and-fry-gene-set-tests"]], "A real-world example": [[23, "a-real-world-example"]], "ADT": [[12, "adt"]], "AIR analysis on RNA clusters": [[3, "air-analysis-on-rna-clusters"]], "AIR repertoire analysis": [[2, "air-repertoire-analysis"]], "API overview": [[19, "api-overview"]], "ATAC": [[12, "atac"]], "Accessing Python from R": [[21, "accessing-python-from-r"]], "Accessing R from Python": [[21, "accessing-r-from-python"]], "Acknowledgements": [[0, null]], "Adding aligned metadata": [[19, "adding-aligned-metadata"]], "Advanced integration": [[27, null]], "Advanced: Multimodal data analysis with muon": [[19, "advanced-multimodal-data-analysis-with-muon"]], "Advanced: Using MuData to store multimodal data": [[19, "advanced-using-mudata-to-store-multimodal-data"]], "Alignment and mapping": [[23, "alignment-and-mapping"]], "Alternative formats": [[30, "alternative-formats"]], "Analysing single-pooled CRISPR screens": [[16, "analysing-single-pooled-crispr-screens"]], "Analysis frameworks and tools": [[19, null]], "Analytic Pearson residuals": [[33, "analytic-pearson-residuals"]], "Annotation": [[5, null], [43, null]], "Annotation by mapping to a reference": [[5, "annotation-by-mapping-to-a-reference"]], "Approaches": [[17, "approaches"], [25, "approaches"]], "Assigning AIR State": [[2, "assigning-air-state"]], "Assumptions & Limitations": [[25, "assumptions-limitations"]], "Atlas building and reference mapping": [[29, "atlas-building-and-reference-mapping"]], "Augur model": [[16, null]], "Authors": [[5, "authors"], [6, "authors"], [7, "authors"], [8, "authors"], [9, "authors"], [11, "authors"], [13, "authors"], [14, "authors"], [15, "authors"], [16, "authors"], [17, "authors"], [19, "authors"], [21, "authors"], [23, "authors"], [24, "authors"], [26, "authors"], [27, "authors"], [28, "authors"], [31, "authors"], [32, "authors"], [33, "authors"], [34, "authors"], [36, "authors"], [37, "authors"], [38, "authors"], [39, "authors"], [40, "authors"], [41, "authors"], [43, "authors"], [44, "authors"], [45, "authors"], [46, "authors"], [47, "authors"], [48, "authors"], [49, "authors"], [50, "authors"]], "Authors:": [[25, "authors"]], "Automated annotation": [[5, "automated-annotation"], [43, "automated-annotation"]], "BCR Data Analysis with Dandelion": [[1, "bcr-data-analysis-with-dandelion"]], "BCR specificity analysis": [[4, "bcr-specificity-analysis"]], "Background": [[17, "background"]], "Batch correction": [[44, null]], "Batch removal complexity": [[7, "batch-removal-complexity"]], "Batch-aware feature selection": [[7, "batch-aware-feature-selection"]], "Benchmarking": [[29, "benchmarking"]], "Benchmarking your own integration": [[7, "benchmarking-your-own-integration"]], "Benisse": [[3, "benisse"]], "Bioconductor": [[21, "bioconductor"]], "Bioconductor OSCA and OSTA books": [[22, "bioconductor-osca-and-osta-books"]], "Brief discussion": [[23, "brief-discussion"]], "Building the index": [[23, "building-the-index"]], "Building the model": [[7, "building-the-model"]], "Building the reference": [[27, "building-the-reference"]], "Bulk deconvolution": [[17, null]], "CITE-seq data": [[28, "cite-seq-data"]], "Calculate a batch-corrected UMAP": [[7, "calculate-a-batch-corrected-umap"]], "Calculate and visualize tumors\u2019 statistics": [[49, "calculate-and-visualize-tumors-statistics"]], "Calculating QC metrics": [[11, "calculating-qc-metrics"]], "Calculating local perturbation signatures": [[16, "calculating-local-perturbation-signatures"]], "Case Study": [[25, "case-study"]], "Case study: Pathway enrichment analysis and activity level scoring in human PBMC single cells": [[15, "case-study-pathway-enrichment-analysis-and-activity-level-scoring-in-human-pbmc-single-cells"]], "Cassiopeia for lineage tracing analysis": [[49, "cassiopeia-for-lineage-tracing-analysis"]], "Cell barcode correction": [[23, "cell-barcode-correction"]], "Cell isolation": [[2, "cell-isolation"]], "Cell-Aligned Data": [[2, "cell-aligned-data"]], "Cell-cell communication": [[25, null]], "Cell-level pathway activity scoring using AUCell": [[15, "cell-level-pathway-activity-scoring-using-aucell"]], "Cell-type specific expression of every gene in the spatial data": [[36, "cell-type-specific-expression-of-every-gene-in-the-spatial-data"]], "Cell2Location cell type mapping": [[36, "cell2location-cell-type-mapping"]], "Cell2Location in practice": [[36, "cell2location-in-practice"]], "Cell2location": [[36, "cell2location"]], "Centered Log-Ratio normalization": [[47, "centered-log-ratio-normalization"]], "Choosing an integration method": [[7, "choosing-an-integration-method"]], "Citation": [[30, "citation"]], "Classifiers based on a wider set of genes": [[5, "classifiers-based-on-a-wider-set-of-genes"]], "Clonal expansion": [[1, "clonal-expansion"]], "Clonal expansion: diversity and abundance": [[1, "clonal-expansion-diversity-and-abundance"]], "Clonotype abundance": [[1, "clonotype-abundance"]], "Clonotype analysis": [[1, null]], "Clonotype definition": [[1, "clonotype-definition"], [1, "id13"]], "Cluster-level gene set enrichment analysis with decoupler": [[15, "cluster-level-gene-set-enrichment-analysis-with-decoupler"]], "Clustering": [[6, null]], "Clustering human bone marrow cells": [[6, "clustering-human-bone-marrow-cells"]], "Co-occurrence across spatial dimensions": [[40, "co-occurrence-across-spatial-dimensions"]], "CoNGA": [[3, "conga"]], "Collecting cellranger outputs into MuData object": [[48, "collecting-cellranger-outputs-into-mudata-object"]], "Combining NicheNet output with ligand-receptor inference": [[25, "combining-nichenet-output-with-ligand-receptor-inference"]], "Common gene set between reference and spatial dataset": [[38, "common-gene-set-between-reference-and-spatial-dataset"]], "Common observations": [[19, "common-observations"]], "Comparisons of data integration methods": [[7, "comparisons-of-data-integration-methods"]], "Compositional analysis": [[13, null]], "Computational tools to interpret time-course lineage tracing data": [[49, "computational-tools-to-interpret-time-course-lineage-tracing-data"]], "Computing the map from single-cells to spatial voxels": [[38, "computing-the-map-from-single-cells-to-spatial-voxels"]], "Conclusions": [[49, "conclusions"]], "Configure data": [[27, "configure-data"]], "Constructing a map between technologies": [[38, "constructing-a-map-between-technologies"]], "Contact us": [[30, "contact-us"]], "Contributing": [[30, "contributing"]], "Contributions": [[25, "contributions"]], "Contributors": [[5, "contributors"], [6, "contributors"], [7, "contributors"], [8, "contributors"], [9, "contributors"], [11, "contributors"], [13, "contributors"], [14, "contributors"], [15, "contributors"], [16, "contributors"], [17, "contributors"], [19, "contributors"], [21, "contributors"], [23, "contributors"], [24, "contributors"], [26, "contributors"], [27, "contributors"], [28, 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"data-normalization"]], "Data preparation": [[7, "data-preparation"]], "Data preprocessing": [[17, "data-preprocessing"], [51, "data-preprocessing"]], "Database Preparation": [[4, "database-preparation"]], "Database Queries": [[4, "database-queries"], [4, "id13"]], "Database query via distance metrics": [[4, "database-query-via-distance-metrics"]], "Dataset": [[2, "dataset"], [7, "dataset"], [11, "dataset"]], "Dataset description": [[26, "dataset-description"]], "Deconvolving bulk COVID-19 whole blood samples": [[17, "deconvolving-bulk-covid-19-whole-blood-samples"]], "Deconvolving using MuSiC": [[17, "deconvolving-using-music"]], "Define neighbourhoods": [[13, "define-neighbourhoods"]], "Determining the most important genes for the prioritization": [[16, "determining-the-most-important-genes-for-the-prioritization"]], "Differential gene expression analysis": [[14, null]], "Differential prioritization": [[16, "differential-prioritization"]], "Dimensionality Reduction": [[31, null], [45, null]], "Discrete tissue regions": [[36, "discrete-tissue-regions"]], "Disk-based interoperability": [[21, "disk-based-interoperability"]], "Distance Measurements": [[4, "distance-measurements"]], "Distances": [[4, "distances"]], "Doublet Detection": [[34, "doublet-detection"]], "Doublet detection": [[11, "doublet-detection"], [23, "doublet-detection"], [46, null]], "Doublets detected with cell type markers": [[46, "doublets-detected-with-cell-type-markers"]], "Down-stream tasks and outlook": [[50, "down-stream-tasks-and-outlook"]], "Downloading the data": [[49, "downloading-the-data"]], "Downstream analysis": [[36, "downstream-analysis"]], "Early stopping": [[7, null]], "Efficient data access": [[19, "efficient-data-access"]], "Empty droplet detection": [[23, "empty-droplet-detection"]], "End-to-end pipelines": [[29, "end-to-end-pipelines"]], "Environment setup": [[5, "environment-setup"], [10, "environment-setup"], [14, "environment-setup"], [17, "environment-setup"], [25, 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"filtering-cells"]], "Filtering features": [[11, "filtering-features"]], "Filtering low quality cells": [[34, "filtering-low-quality-cells"]], "Filtering out low-quality tumors": [[49, "filtering-out-low-quality-tumors"]], "Filtering out the gene sets with low number of genes": [[15, "filtering-out-the-gene-sets-with-low-number-of-genes"]], "First-generation sequencing": [[24, "first-generation-sequencing"]], "Fitting the reference model": [[36, "fitting-the-reference-model"]], "Fluidigm C1": [[24, "fluidigm-c1"]], "Formation of adaptive immune receptors by V(D)J recombination": [[2, "formation-of-adaptive-immune-receptors-by-v-d-j-recombination"]], "From cluster differentially expressed genes to cluster annotation": [[5, "from-cluster-differentially-expressed-genes-to-cluster-annotation"]], "From markers to cluster annotation": [[5, "from-markers-to-cluster-annotation"]], "Further Models in Reference Based Deconvolution": [[36, "further-models-in-reference-based-deconvolution"]], "GEX analysis on AIR clusters": [[3, "gex-analysis-on-air-clusters"]], "Gamma-Poisson distribution": [[33, null]], "Gathering TF regulons from public data": [[26, "gathering-tf-regulons-from-public-data"]], "Gene regulatory network inference using RNA and ATAC features": [[8, "gene-regulatory-network-inference-using-rna-and-atac-features"]], "Gene regulatory networks": [[26, null]], "Gene regulatory networks using chromatin accessibility": [[8, null]], "Gene segment usage": [[1, "gene-segment-usage"]], "Gene segment usage and spectratype": [[1, "gene-segment-usage-and-spectratype"]], "Gene set enrichment and pathway analysis": [[15, null]], "Gene set enrichment for complex experimental designs using limma-fry and pseudo-bulks": [[15, "gene-set-enrichment-for-complex-experimental-designs-using-limma-fry-and-pseudo-bulks"]], "Gene set test vs. pathway activity inference": [[15, "gene-set-test-vs-pathway-activity-inference"]], "Gene set tests and pathway analysis": [[15, "gene-set-tests-and-pathway-analysis"]], "Gene usage": [[1, "gene-usage"]], "General remarks": [[5, "general-remarks"]], "General settings": [[51, "general-settings"]], "Generating a Ligand-Receptor consensus with LIANA": [[25, "generating-a-ligand-receptor-consensus-with-liana"]], "Generation of GRNs using RNA data": [[26, "generation-of-grns-using-rna-data"]], "Glossary": [[18, null]], "Graph construction": [[27, "graph-construction"]], "Graph-based integration": [[7, "graph-based-integration"]], "H5AD": [[21, "h5ad"]], "HDF5-based formats": [[21, "hdf5-based-formats"]], "Harmony": [[44, "harmony"]], "How many genes to use?": [[7, null]], "Hyperparameters of SpaGCN": [[37, "hyperparameters-of-spagcn"]], "IRs of the adaptive immune system": [[2, "irs-of-the-adaptive-immune-system"]], "Identical matches": [[4, "identical-matches"]], "Identifying cells with no detectable perturbation": [[16, "identifying-cells-with-no-detectable-perturbation"]], "Identifying interactions between spatial communities": [[40, "identifying-interactions-between-spatial-communities"]], "Identifying the cell types most affected by perturbations": [[16, "conditions-perturbation-modeling-key-takeaway-1"]], "Immune Receptor Profiling": [[2, null]], "Immune receptor sequencing": [[2, "immune-receptor-sequencing"]], "Imputation": [[38, null]], "Imputing genes and mapping cell-types to space": [[38, "imputing-genes-and-mapping-cell-types-to-space"]], "In-memory interoperability": [[21, "in-memory-interoperability"]], "Inferring expansion events": [[49, "inferring-expansion-events"]], "Inferring pseudotime for adult human bone marrow": [[50, "inferring-pseudotime-for-adult-human-bone-marrow"]], "Inferring tree plasticity": [[49, "inferring-tree-plasticity"]], "Initializing a MuData object": [[19, "initializing-a-mudata-object"]], "Initializing an AnnData object": [[19, "initializing-an-anndata-object"]], "Inspecting quality control metrics": [[31, "inspecting-quality-control-metrics"]], "Install 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Acknowledgements", "39. Clonotype analysis", "38. Immune Receptor Profiling", "44. Integrating AIR and transcriptomics", "43. Specificity analysis", "11. Annotation", "10. Clustering", "12. Data integration", "25. Gene regulatory networks using chromatin accessibility", "23. Single-cell ATAC sequencing", "Conversion of muon objects to Seurat objects to use in downstream analysis", "24. Quality Control", "Markers for cluster annotations across modalities", "17. Compositional analysis", "16. Differential gene expression analysis", "18. Gene set enrichment and pathway analysis", "19. Perturbation modeling", "22. Bulk deconvolution", "50. Glossary", "4. Analysis frameworks and tools", "Data infrastructure", "5. Interoperability", "1. Prior art", "3. Raw data processing", "2. Single-cell RNA sequencing", "21. Cell-cell communication", "20. Gene regulatory networks", "46. Advanced integration", "45. Paired integration", "48. Outlook", "Single-cell best practices", "9. 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[7, 19, 49], "metric": [4, 11, 28, 31], "microfluid": 24, "mnn": 7, "modal": [3, 12, 29], "model": [3, 7, 16, 25, 36, 49, 51], "mofa": 28, "moran": 41, "more": 36, "most": 16, "motif": 1, "motiv": [3, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 21, 23, 25, 26, 27, 28, 32, 33, 34, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51], "mous": 49, "mudata": [10, 19, 48], "multi": [28, 39], "multigr": 27, "multimod": [3, 19, 21], "multiom": 28, "multipl": 14, "multivi": 28, "muon": [10, 19], "music": 17, "mutual": 7, "mvtcr": 3, "nanopor": 24, "nearest": [7, 28], "need": 23, "neighbor": [7, 28], "neighborhood": 40, "neighbourhood": 13, "network": [8, 26], "neurip": 26, "new": [17, 21, 49, 51], "ng": 24, "nichenet": 25, "nomenclatur": 21, "normal": [15, 33, 47], "note": [7, 14, 15, 23, 24], "nuclei": 24, "nucleosom": 11, "null": 15, "number": [11, 15, 49], "object": [10, 19, 48], "observ": 19, "occurr": 40, "omic": 28, "onto": 27, "order": 50, "orient": 23, "osca": 22, "osta": 22, "other": 21, "out": [15, 49], "outcom": 26, "outlook": [25, 29, 50], "output": [3, 17, 25, 48], "overdispers": 33, "overlap": 27, "overview": [9, 19, 24, 39, 49], "own": 7, "packag": 8, "pair": 28, "pancreat": 51, "paramet": 51, "part": 38, "partial": [19, 27], "pathwai": 15, "pbmc": 15, "pca": [31, 45], "pearson": 33, "peer": 30, "per": 49, "perform": [11, 15], "perturb": 16, "phylogenet": 49, "pipelin": [23, 29, 49], "plastic": 49, "plate": 24, "plot": 38, "png": 8, "poisson": 33, "pool": 16, "potenti": 25, "practic": [22, 30, 36], "practis": 38, "pre": 36, "preced": 23, "predict": [4, 16, 25, 29], "prepar": [1, 3, 4, 7, 8, 14, 15, 23, 26, 27, 28, 49], "preprocess": [3, 16, 17, 37, 51], "prerank": 15, "prerequisit": 30, "prior": [22, 25], "priorit": 16, "process": [23, 24, 36], "product": 2, "profil": [2, 39], "properti": 49, "proteom": 29, "protocol": 24, "pseudo": 15, "pseudobulk": 14, "pseudotempor": 50, "pseudotim": 50, "public": 26, "python": [7, 21], "qc": [11, 48], "qualiti": [2, 11, 23, 31, 34, 48, 49], "quantif": [23, 24], "quantifi": 49, "queri": [4, 27], "quiz": [2, 3, 4, 7, 8, 13, 14, 15, 16, 25, 26], "r": [7, 17, 21], "ratio": 47, "raw": [2, 23], "rd": 21, "read": [10, 19, 21, 30, 39], "real": 23, "receiv": 25, "receptor": [2, 25], "recombin": 2, "recommend": 39, "reconstruct": 49, "reduct": [31, 45], "redund": 15, "refer": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51], "refin": 37, "region": 36, "regulatori": [8, 25, 26], "regulon": 26, "remark": 5, "remov": [7, 13], "repertoir": [1, 2], "represent": 23, "reproduc": 35, "residu": 33, "resolut": [23, 39], "resolv": 39, "resourc": 49, "respons": 16, "result": [8, 26], "retriev": 15, "review": [5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 19, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50], "rna": [3, 8, 12, 22, 24, 26, 27, 34, 51], "role": 2, "run": [3, 13, 15, 17], "rust": 21, "sampl": [15, 17, 48], "save": 8, "scalabl": 7, "scanpi": 19, "scenic": 26, "scgen": 16, "scib": 28, "score": [11, 15, 41], "screen": 16, "second": 24, "segment": 1, "select": [7, 32, 49], "sender": 25, "seq": [22, 28], "sequenc": [1, 2, 9, 23, 24], "session": [7, 15, 21, 25, 27], "set": [5, 15, 16, 25, 38, 51], "setup": [5, 10, 14, 15, 17, 25, 26, 27, 28, 34, 37, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51], "seurat": [10, 21, 27], "shift": 33, "should": 30, "signal": [11, 25], "signatur": 16, "silicon": 23, "simpl": 21, "simplifi": 23, "singl": [9, 14, 15, 16, 17, 19, 22, 24, 29, 30, 36, 38, 39], "singlecellexperi": 8, "size": 49, "sne": 31, "sourc": 25, "space": [38, 39], "spagcn": 37, "sparsiti": 9, "spatal": 36, "spatial": [36, 37, 38, 39, 40, 41], "spatiald": 41, "specif": [4, 14, 36], "spectratyp": 1, "splice": 23, "squidpi": [37, 41], "state": [2, 51], "statist": 49, "steadi": 51, "step": [23, 25], "stereoscop": 36, "stimul": [15, 16], "stop": 7, "store": 19, "stream": 50, "strict": 4, "structur": [13, 30], "studi": [15, 25], "sub": 39, "subset": 19, "summari": [24, 25], "system": 2, "t": [16, 31], "takeawai": [25, 49], "tangram": 38, "target": 25, "task": 50, "tcr": [1, 3, 4], "tcrdist": 4, "tcrmatch": 4, "technic": 15, "technologi": [38, 49], "tessa": 3, "test": [13, 15], "tf": 26, "theori": [8, 26], "thi": 30, "third": 24, "threshold": 11, "time": 49, "tissu": 36, "tool": [19, 49], "top": 25, "total": [11, 28], "totalvi": [27, 28], "trace": 49, "train": [7, 16, 38], "transcript": 24, "transcriptom": [3, 23, 24], "trap": 17, "tree": 49, "trimod": 27, "truth": 7, "tss": 11, "tumor": 49, "tutori": 22, "two": 15, "type": [7, 13, 15, 16, 23, 25, 36, 38, 46], "u": 30, "umap": [7, 31, 45], "umi": [7, 23], "uni": 3, "unifi": 27, "unimod": 19, "unintegr": 7, "unpair": 27, "unstructur": 19, "up": 16, "upper": 11, "us": [7, 8, 10, 15, 17, 19, 23, 26, 38], "usag": 1, "v": [2, 15, 24], "vae": 7, "valid": [17, 38], "variabl": [19, 41], "variat": [7, 16, 28], "variou": 4, "vdj": 2, "veloc": 51, "via": 4, "view": 19, "visual": [2, 8, 14, 16, 17, 25, 49], "voxel": 38, "warn": 5, "weight": 28, "were": 38, "what": [7, 13, 30], "who": 30, "whole": 17, "why": 13, "wider": 5, "wise": 48, "without": 13, "wnn": [27, 28], "workflow": 9, "world": 23, "write": [19, 21], "your": 7, "zellkonvert": 8, "\u03b2": 16}}) \ No newline at end of file diff --git a/pr-preview/pr-344/trajectories/pseudotemporal.html b/pr-preview/pr-344/trajectories/pseudotemporal.html index cc3155b6..8c75f79e 100644 --- a/pr-preview/pr-344/trajectories/pseudotemporal.html +++ b/pr-preview/pr-344/trajectories/pseudotemporal.html @@ -601,7 +601,7 @@

13. Pseudotemporal ordering -Access to data and notebook
+   Access to data and notebook

This book uses lamindb to store, share, and load datasets and notebooks using the theislab/sc-best-practices instance. We acknowledge free hosting from Lamin Labs.

    @@ -649,11 +649,12 @@

    13. Pseudotemporal orderingLoad an Artifact and the corresponding object:

    import lamindb as ln
-af = ln.Artifact.get(key="key_of_dataset", is_latest=True)
+af = ln.Artifact.get(key="key_of_dataset", is_latest=True)  # or ln.Artifact("SOMEID").get()
 obj = af.load()
    -

    The object is now accessible in memory and is ready for analysis.

    +

    The object is now accessible in memory and is ready for analysis. +Adapt the ln.Artifact("SOMEID").get() suffix to get older versions like ln.Artifact("SOMEID0001").get() to get the second uploaded version.

  1. Accessing notebooks (Transforms)

-

which will download the notebook to the current working directory.

+

which will download the notebook to the current working directory. +Analogously to Artifacts, you can adapt the suffix ID to get older versions.

-

  • **On ln.track() and ln.finish()

    +

  • On ln.track() and ln.finish()

    • These functions are currently only available for users with write access and may error. Please comment them out for now.