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inopenproblems-bio/openproblems (press backspace or delete to remove)Task Motivation
Single-cell RNA sequencing allows for unprecedented resolution in studying cellular heterogeneity and gene expression
dynamics. However, analyzing data from multiple experiments is often ...
help wanted
task
rcannood
- Opened on Sep 29, 2024
- #906
See https://openproblems.bio/datasets/10x_datasets/human_cerebellum_visium/
bug
- Opened on Sep 18, 2024
- #905
Task motivation
Spatially resolved transcriptomics offers unprecedented insight by enabling the profiling of gene expression within the
intact spatial context of cells, effectively adding a new and essential ...
task
lzj1769
- 1
- Opened on Mar 12, 2024
- #901
Task motivation
The growing availability of single-cell data has sparked an increased interest in the inference of cell-cell
communication (CCC), with an ever-growing number of computational tools developed ...
task
vishnu-vasan
- 2
- Opened on Feb 14, 2024
- #903
Task motivation
Spatial decomposition (also often referred to as Spatial deconvolution) is applicable to spatial transcriptomics data
where the transcription profile of each capture location (spot, voxel, ...
task
danielStrobl
- 4
- Opened on Aug 30, 2023
- #902
SVM was best performing method in Abdelaal et al., 2019
enhancement
Stale
mxposed
- 1
- Opened on Mar 26, 2023
- #862
The task-specific datasets have metadata (link) that are not included in the data loaders (link). In v2, we are
currently using an additional yaml (link) to add metadata by default. Is it okay if we add ...
Stale
KaiWaldrant
- 2
- Opened on Mar 15, 2023
- #855
New method (+benchmark paper) at https://www.nature.com/articles/s41467-023-35923-4
cc @mxposed
enhancement
Stale
scottgigante-immunai
- 3
- Opened on Mar 14, 2023
- #852
- [x] I have checked that this issue has not already been reported.
- [x] I have confirmed this bug exists on the main branch of openproblems.
CI run_tester fails for all tasks, see here
Error:
...
bug
- Opened on Feb 15, 2023
- #830
What is the method? A hierarhical variational autoencoder that reconstructs LR expression and full profiles to assess
how well cells can be reconstructed from their LR-profiles alone to estimate interaction ...
enhancement
LuckyMD
- 1
- Opened on Feb 13, 2023
- #829
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