adding tables to adata.obs and subsetting #150

StasMakarchuk · 2025-01-09T16:55:30Z

Added possibility to add custom csv table to adata.obs (for example cell types or clustering outputs). Make sure that csv file contatins column with correct cell identifiers and specify this column name
Subsetting of xenium and spaceranger datasets - both in anndata and in image label file. We keep original cell ids, so subsetted set of cell ids (numbers) may have "gaps", like 1,2,3,5,9,....

added possibility to add columns in adata.obs and subsetting in visium and xenium

make sure spot id becomes column, and indeces are integer numbers starting with 1

envs/build-docker-imgs.sh

envs/Dockerfile

main.nf

bin/process_spaceranger.py

bin/process_xenium.py

sphinx/installation.rst

StasMakarchuk added 24 commits November 8, 2024 15:44

Add files via upload

801eff9

added possibility to add columns in adata.obs and subsetting in visium and xenium

Update process_h5ad.py

dcc1627

Update process_spaceranger.py

13cf164

Create conf_xenium_subset.yaml

756d18e

Create visium_conf_subset.yaml

f0cb990

Update process_spaceranger.py

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make sure spot id becomes column, and indeces are integer numbers starting with 1

Update process_spaceranger.py

2a7613b

Update generate_image.py

20c3ec0

Update process_xenium.py

5a515bd

fixed bug with index

c92adb4

Update Dockerfile

d03db9c

Update build-docker-imgs.sh

8b985a1

Update main.nf

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Update multimodal.nf

de8aa42

Update nextflow.config

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Update visium.rst

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Update xenium.rst

b2987e9

Update installation.rst

f4cd625

Update process_h5ad.py

f613d74

Update process_spaceranger.py

28a0fd9

Update process_xenium.py

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Update process_xenium.py

ee0ea24

Update process_spaceranger.py

32edf8a

Update configuration.rst

1da9bbe

prete requested changes Jan 9, 2025

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StasMakarchuk added 5 commits February 25, 2025 15:10

Update process_spaceranger.py

f011c00

Update process_xenium.py

496d1c8

Update process_xenium.py

de5873b

Create visum_subset_template.yaml

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Create xenium_subset_template.yaml

6de342b

StasMakarchuk added 11 commits February 25, 2025 15:16

Delete conf directory

47a891b

Update Dockerfile

6ece93e

Update environment.yaml

fc211a7

Update build-docker-imgs.sh

cb4b3e6

Update main.nf

364610b

Update nextflow.config

252c7ae

Update configuration.rst

00e4a24

Update visium.rst

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Update xenium.rst

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Update xenium.rst

ae82d96

Update installation.rst

b1657a3

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adding tables to adata.obs and subsetting #150

adding tables to adata.obs and subsetting #150

StasMakarchuk commented Jan 9, 2025

adding tables to adata.obs and subsetting #150

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adding tables to adata.obs and subsetting #150

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StasMakarchuk commented Jan 9, 2025