Comments (5)
@bioworker, as I have tested, conda will install the newest version. You can paste your installation information here if you still fail to install the newest CellTypist.
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@bioworker, as I have tested, conda will install the newest version. You can paste your installation information here if you still fail to install the newest CellTypist.
Ok, The version information suggested the newest one (1.3.0), but it lack the methods like extract_top_markers, did you check this method? Now I have reinstalled it by pip command, everything is fine now.
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Can confirm that latest conda-installed version is working.
Instaled using:
conda install -c bioconda -c conda-forge celltypist
Then:
>>> import celltypist
>>> celltypist.__version__
'1.3.0'
>>> model = celltypist.models.Model.load(model = 'Immune_All_Low.pkl')
>>> model.extract_top_markers("Mast cells", 3)
array(['CPA3', 'TPSAB1', 'FTH1'], dtype=object)
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Hi there - I also encountered this issue, but I believe it's Mac apple silicon dependent. when I run:
conda install -c bioconda -c conda-forge celltypist
My install completes, but to 0.1.9.
However, when I run:
conda install -c bioconda -c conda-forge celltypist=1.3
I get the following solve error:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
- feature:/osx-arm64::__unix==0=0
- celltypist=1.3 -> click[version='>=7.1.2'] -> __unix
- celltypist=1.3 -> click[version='>=7.1.2'] -> __win
Your installed version is: 0
FYI - pip install works fine
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Indeed it seems to be a Mac M1/M2 issue. The arm architecture probably has conflicting packages.
To solve this issue they can try rosetta. Useful links here and here. Rosetta should translate intel instructions and if they are using conda, they should make sure that the right conda installer (ARM version) is used. The info in this issue can also help.
Otherwise, and as you mentioned, sticking with pip should not give you any issues.
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Related Issues (20)
- codes for harmonizing the cell labels HOT 2
- the question about conf_score HOT 3
- CellTypist_Immune_Reference_v2 question HOT 2
- Immune_All_Low - model training question HOT 4
- Cluster-level label prediction HOT 1
- Running celltypist with concatenated dataset HOT 3
- Running the CellTypist training function celltypist.train on a subset of genes HOT 1
- ValueError in celltypist.annotate HOT 3
- is it available to generate model.pkl file from a marker gene list HOT 1
- Feature: Support Rapids-singlecell HOT 1
- Can not detect a neighborhood graph, will construct one before the over-clustering HOT 1
- multiple models HOT 3
- Question about over_clustering and conf_score? HOT 1
- Conflict with variable genes and model training HOT 1
- www.celltypist.org is down, cannot download models HOT 3
- Can not download the model HOT 2
- Very low confidence score even though labels are correct HOT 2
- celltypist before/after batch correction HOT 4
- Issue accessing www.celltypist.org - 502 Bad Gateway HOT 5
- Organ atlas Citing CellTypist. Automatic cell type harmonization and integr… HOT 1
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