scTriangulate
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frankligy
scTriangulate is a Python package to mix-and-match conflicting clustering results in single cell analysis and generate reconciled clustering solutions
right now gsea run is required, but actually it is not part of the core algorithm of scTriangulate but just for visuliazation purpouse.
https://github.com/Barski-lab/workflows/blob/master/tools/dockerfiles/scripts/sc_split_atac.py instead of using pool, use shared_memory to reduce memory overhead
It seems there's some weird bug in test.py code. Could you take a look and see why it happens? I ran it on my Mac: ``` P14-5847:sctriangulate_test kang$ /Users/kang/miniconda3/envs/aipy/bin/python3.7 -W...
1. need rust please refer to (https://github.com/zqfang/GSEApy/issues/163)
Hello, I'm going through the tutorial (https://sctriangulate.readthedocs.io/en/latest/tutorial.html), with provided h5 file (http://altanalyze.org/scTriangulate/scRNASeq/pbmc_10k_v3.h5). I use Jupyter notebook (Python 3.9.18) and work in a server - 8 cores and memory of 128GB...
It has been brought to my attention that a new change post pandas v2 will break the gseapy function due to the deprecated `.append()` function, you may encounter error like...
I ran my code on windows system. Here are the errors: File "", line 1, in File "C:\Users\jiabl9\Anaconda3\envs\scTriangulate\lib\site-packages\sctriangulate\main_class.py", line 972, in compute_metrics subprocess.run(['rm','-r','{}'.format(os.path.join(self.dir,'scTriangulate_local_mode_enrichr/'))]) File "C:\Users\jiabl9\Anaconda3\envs\scTriangulate\lib\subprocess.py", line 493, in run with...
>>> adata.write('test.h5ad') ``` Traceback (most recent call last): File "/opt/anaconda3/envs/sctri_env/lib/python3.7/site-packages/anndata/_io/utils.py", line 214, in func_wrapper return func(elem, key, val, *args, **kwargs) File "/opt/anaconda3/envs/sctri_env/lib/python3.7/site-packages/anndata/_io/specs/registry.py", line 175, in write_elem _REGISTRY.get_writer(dest_type, t, modifiers)(f, k,...
Hello I tried to pip install the package in spyder. But it failed, below is lines from console. tried .whl or the .gz, both failed. pip install scTriangulate Collecting scTriangulate...
instead of specifying human or mouse, let the program directly detect and determine that.