From 1457a6306efe95ebd09da2bada475caac0af2187 Mon Sep 17 00:00:00 2001 From: Linbu Date: Thu, 27 Jul 2023 14:09:35 +0200 Subject: [PATCH 1/3] Create meta.yaml Mandatory Name of the tool: SC2Spa Short description: SC2Spa is a deep learning-based tool to predict the spatial coordinates of single cells. How does the package use scverse data structures (please describe in a few sentences): scanpy and anndata are used for preprocessing for SC2Spa. SquidPy is used to calculate Moran's I in the downstream analysis of SC2Spa. The code is publicly available under an OSI-approved license Yes, SC2Spa is under BSD 3-Clause license The package provides versioned releases Yes The package can be installed from a standard registry (e.g. PyPI, conda-forge, bioconda) Yes, SC2Spa can be installed from PyPI The package uses automated software tests and runs them via continuous integration (CI) Yes The package provides API documentation via a website or README Yes The package uses scverse datastructures where appropriate (i.e. AnnData, MuData or SpatialData and their modality-specific extensions) Yes, SC2Spa uses AnnData, SCANPY and SquidPy I am the author or maintainer of the tool and agree on listing the package on the scverse website Yes Recommended I would like this package to be announced on scverse channels (zulip, discourse, twitter) [Include twitter handles you want us to tag]: Yes, I would recommend these handles: SC2Spa, Spatial Inference, scRNA-seq, spatial transcriptomics, predict spatial coordinates, cell communication. The package provides tutorials (or "vignettes") that help getting users started quickly Yes, SC2Spa provides readthedocs tutorials. The package uses the scverse cookiecutter template. No, but I will consider adding this feature in the future --- packages/SC2Spa/meta.yaml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 packages/SC2Spa/meta.yaml diff --git a/packages/SC2Spa/meta.yaml b/packages/SC2Spa/meta.yaml new file mode 100644 index 0000000..271573d --- /dev/null +++ b/packages/SC2Spa/meta.yaml @@ -0,0 +1,25 @@ +name: SC2Spa +description: | + SC2Spa is a deep learning-based tool for predicting the spatial coordinates of single cells based on transcriptome. + Two paired single cell and spatial transcriptomic datasets are required to run SC2Spa. SC2Spa is trained on a ST reference + dataset to learn the relationship of gene expression and spatial coordinates. The trained fully-connected neural network + can be used to predict the locations of a single cell with only the transcriptomic profile as input. The predicted locations + of single cells can be further used to study the communication of the single cells. +project_home: https://github.com/linbuliao/SC2Spa +documentation_home: https://sc2spa.readthedocs.io/ +publications: + - +install: + pypi: SC2Spa +tags: + - spatial inference + - scRNA-seq + - spatial transcriptomics + - deep learning + - cell communication +license: BSD 3-Clause +version: v1.2 +authors: + - Linbu Liao + - Kyoung Jae Won +test_command: pip install "." && pytest From 3af9cafd3aef4d37588dbe55bbf83a0b3479ced2 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 27 Jul 2023 12:10:06 +0000 Subject: [PATCH 2/3] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- packages/SC2Spa/meta.yaml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/packages/SC2Spa/meta.yaml b/packages/SC2Spa/meta.yaml index 271573d..0b417a2 100644 --- a/packages/SC2Spa/meta.yaml +++ b/packages/SC2Spa/meta.yaml @@ -1,22 +1,22 @@ name: SC2Spa description: | - SC2Spa is a deep learning-based tool for predicting the spatial coordinates of single cells based on transcriptome. - Two paired single cell and spatial transcriptomic datasets are required to run SC2Spa. SC2Spa is trained on a ST reference - dataset to learn the relationship of gene expression and spatial coordinates. The trained fully-connected neural network - can be used to predict the locations of a single cell with only the transcriptomic profile as input. The predicted locations - of single cells can be further used to study the communication of the single cells. + SC2Spa is a deep learning-based tool for predicting the spatial coordinates of single cells based on transcriptome. + Two paired single cell and spatial transcriptomic datasets are required to run SC2Spa. SC2Spa is trained on a ST reference + dataset to learn the relationship of gene expression and spatial coordinates. The trained fully-connected neural network + can be used to predict the locations of a single cell with only the transcriptomic profile as input. The predicted locations + of single cells can be further used to study the communication of the single cells. project_home: https://github.com/linbuliao/SC2Spa documentation_home: https://sc2spa.readthedocs.io/ publications: - - + - install: - pypi: SC2Spa + pypi: SC2Spa tags: - - spatial inference - - scRNA-seq - - spatial transcriptomics - - deep learning - - cell communication + - spatial inference + - scRNA-seq + - spatial transcriptomics + - deep learning + - cell communication license: BSD 3-Clause version: v1.2 authors: From e7c5e9e7fd03ab2dd9e3bbea68a3651d19980cf6 Mon Sep 17 00:00:00 2001 From: Linbu Date: Thu, 27 Jul 2023 14:17:58 +0200 Subject: [PATCH 3/3] Update Add SC2Spa --- packages/SC2Spa/meta.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/packages/SC2Spa/meta.yaml b/packages/SC2Spa/meta.yaml index 0b417a2..9fd80d6 100644 --- a/packages/SC2Spa/meta.yaml +++ b/packages/SC2Spa/meta.yaml @@ -7,8 +7,6 @@ description: | of single cells can be further used to study the communication of the single cells. project_home: https://github.com/linbuliao/SC2Spa documentation_home: https://sc2spa.readthedocs.io/ -publications: - - install: pypi: SC2Spa tags: @@ -17,7 +15,7 @@ tags: - spatial transcriptomics - deep learning - cell communication -license: BSD 3-Clause +license: BSD-3-Clause version: v1.2 authors: - Linbu Liao