pyrovelocity.io.datasets#
- pyrovelocity.io.datasets.bonemarrow(file_path='data/external/bonemarrow.h5ad')[source]#
Human bone marrow data sourced from the scvelo library.
Data from Setty et al. (2019) will be downloaded from
https://ndownloader.figshare.com/files/27686835
- Parameters:
file_path (str, optional) – Path to save file. Defaults to “data/external/bonemarrow.h5ad”.
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.larry(file_path='data/external/larry.h5ad')[source]#
In vitro hematopoiesis LARRY dataset.
Data from `Weinreb et al. (2020) <DOI: 10.1126/science.aaw3381>’ https://figshare.com/ndownloader/articles/20780344/versions/1
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.larry_cospar(file_path='data/external/larry_cospar.h5ad')[source]#
In vitro hematopoiesis LARRY dataset with cospar-based fate estimates.
Subset of Data from `Weinreb et al. (2020) <DOI: 10.1126/science.aaw3381>’
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.larry_cytotrace(file_path='data/external/larry_cytotrace.h5ad')[source]#
In vitro hematopoiesis LARRY dataset with cytotrace-based fate estimates.
Subset of Data from `Weinreb et al. (2020) <DOI: 10.1126/science.aaw3381>’
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.larry_dynamical(file_path='data/external/larry_dynamical.h5ad')[source]#
The LARRY in vitro hematopoiesis dataset with scvelo dynamical model output.
Subset of Data from `Weinreb et al. (2020) <DOI: 10.1126/science.aaw3381>’
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.larry_mono(file_path='data/external/larry_mono.h5ad')[source]#
In vitro hematopoiesis LARRY dataset Subset of Data from `Weinreb et al. (2020) <DOI: 10.1126/science.aaw3381>’ consisting of unipotent monocyte precursors and monocytes.
https://figshare.com/ndownloader/files/37028572
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.larry_multilineage(file_path='data/external/larry_multilineage.h5ad')[source]#
The monocyte and neutrophil subset of the LARRY in vitro hematopoiesis dataset.
Subset of Data from `Weinreb et al. (2020) <DOI: 10.1126/science.aaw3381>’
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.larry_neu(file_path='data/external/larry_neu.h5ad')[source]#
In vitro hematopoiesis LARRY dataset.
Subset of Data from `Weinreb et al. (2020) <DOI: 10.1126/science.aaw3381>’ consisting of unipotent neutrophil precursors and neutrophils.
https://figshare.com/ndownloader/files/37028575
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.larry_tips(file_path='data/external/larry_tips.h5ad')[source]#
The differentiated subset of the LARRY in vitro hematopoiesis dataset.
Subset of Data from `Weinreb et al. (2020) <DOI: 10.1126/science.aaw3381>’
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.pancreas(file_path='data/external/pancreas.h5ad')[source]#
Pancreatic endocrinogenesis data sourced from the scvelo library.
Data from Bastidas-Ponce et al. (2019) will be downloaded from
https://github.com/theislab/scvelo_notebooks/raw/master/data/Pancreas/endocrinogenesis_day15.h5ad
- Parameters:
file_path (str, optional) – Path to save file. Defaults to “data/external/pancreas.h5ad”.
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.pbmc10k(file_path='data/external/pbmc10k.h5ad')[source]#
10x genomics 10k Human PBMCs.
https://www.10xgenomics.com/datasets/10k-human-pbmcs-3-ht-v3-1-chromium-x-3-1-high
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.pbmc5k(file_path='data/external/pbmc5k.h5ad')[source]#
10x genomics 5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor.
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.pbmc68k(file_path='data/external/pbmc68k.h5ad')[source]#
Peripheral blood mononuclear cells data sourced from the scvelo library.
Data from Zheng et al. (2017) will be downloaded from
https://ndownloader.figshare.com/files/27686886
- Parameters:
file_path (str, optional) – Path to save file. Defaults to “data/external/pbmc68k.h5ad”.
- Return type:
AnnData- Returns:
Returns AnnData object
- pyrovelocity.io.datasets.pons(file_path='data/external/pons.h5ad')[source]#
Pons oligodendrocyte data from La Manno et al. (2018).
Data originally obtained from https://pklab.med.harvard.edu/ruslan/velocity/oligos/oligos_info.rds and converted to AnnData format.
- Return type:
AnnData- Returns:
Returns AnnData object