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Merged
ghar1821 merged 6 commits into from
Oct 9, 2025
Merged

Add new dataset #106

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92a0131
add dataset processing script
rcannood Sep 30, 2025
e87bc73
fix reference
rcannood Sep 30, 2025
cc03dc7
add goal batch
ghar1821 Sep 30, 2025
ae51580
update script for cll dataset
ghar1821 Oct 7, 2025
c5da055
Merge branch 'main' into add-dataset
ghar1821 Oct 9, 2025
81d2cc2
update changelog
ghar1821 Oct 9, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -64,6 +64,7 @@

* Added Seurat rPCA (PR #95).

* Added processing scripts for CLL dataset (PR #106).

## MAJOR CHANGES

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36 changes: 36 additions & 0 deletions scripts/create_resources/human_cll_mass_cytometry.sh
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#!/bin/bash

# get the root of the directory
REPO_ROOT=$(git rev-parse --show-toplevel)

# ensure that the command below is run from the root of the repository
cd "$REPO_ROOT"

set -e

RAW_DIR=resources_raw/human_cll_mass_cytometry/
DATASET_ID=human_cll_mass_cytometry
OUTPUT_DIR=resources/datasets_raw/$DATASET_ID/

mkdir -p $OUTPUT_DIR

# create raw dataset files
python << HERE
import anndata as ad

adata = ad.read_h5ad("$RAW_DIR/human_cll_mass_cytometry.h5ad")

# make sure the output is compressed
adata.write_h5ad("$OUTPUT_DIR/common_dataset.h5ad", compression='gzip')
HERE

cat > $OUTPUT_DIR/state.yaml << HERE
id: $DATASET_ID
output_dataset: !file common_dataset.h5ad
HERE

# only run this if you have access to the openproblems-data bucket
aws s3 sync --profile op \
resources/datasets_raw/human_cll_mass_cytometry \
s3://openproblems-data/resources/task_cyto_batch_integration/datasets_raw/human_cll_mass_cytometry/ \
--delete --dryrun