some files

Author: craniolab

notes.txt

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+install specific github commit
+remotes::install_github("satijalab/seurat-wrappers@73466e361ee759c6b1add58faa3bc4e7a2ee5753") 
+
+
+Sys.setenv(GITHUB_PAT="/home/jupyter-seton/micromamba/envs/seurat_v5/bin:/opt/tljh/user/condabin:/opt/tljh/user/bin:/opt/tljh/user/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/sbin:/usr/bin:/snap/bin"
+
+important package for compiling
+micromamba install pkg-config
+
+python -m ipykernel install --user --name myenv --display-name myenv
+
+IRkernel::installspec(name = 'myenv', displayname = 'myenv')
+
+to save plotly figures, have to add the kaleido folder to path
+os.environ["PATH"] += os.pathsep + "/home/jupyter-seton/micromamba/envs/cellrank/bin"

sequencing_results_loc.txt

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+ME8,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23120362-Z01-F002/ME8/outs/filtered_feature_bc_matrix
+ME9,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23064848-Z01-F003/Mouse_filtered_3/ME9/outs/filtered_feature_bc_matrix
+ME10,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23120362-Z01-F002/ME10/outs/filtered_feature_bc_matrix
+ME11,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23064848-Z01-F003/Mouse_filtered_3/ME11/outs/filtered_feature_bc_matrix
+ME12,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23064848-Z01-F003/Mouse_filtered_3/ME12/outs/filtered_feature_bc_matrix
+RE8,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23120362-Z01-F002/RE8/outs/filtered_feature_bc_matrix
+RE9,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23120362-Z01-F002/RE9/outs/filtered_feature_bc_matrix
+RE10,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23120362-Z01-F002/RE10/outs/filtered_feature_bc_matrix
+RE11,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23120362-Z01-F002/RE11/outs/filtered_feature_bc_matrix
+RE12,/mnt/mpistaff/Cranio_Lab/Louk_Seton/IMPORTANT_DATA_DONT_DELETE/X204SC23120362-Z01-F002/RE12/outs/filtered_feature_bc_matrix