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Update Data processing and plotting/Image analysis data processing and plotting/Figure 5I - LaminB1 staining/Environment.RData, Data processing and plotting/Image analysis data processing and plotting/Figure 5I - LaminB1 staining/LMNB1 stainings.Rmd
Update MEA analysis/Environment.RData, MEA analysis/MEA_per_electrode.Rmd, MEA analysis/MEA_per_electrode.nb.html, Metabolic modelling/Matlab files scripts/CountReconSubsystems.mlx, Metabolic modelling/Matlab files scripts/fastcormicsRNAseq.mlx, Metabolic modelling/Matlab files scripts/Model_comarison_2xWTvs2xMUT.mlx, Metabolic modelling/Matlab files scripts/modelMUTKT16.mat, Metabolic modelling/Matlab files scripts/modelWT56.mat, Metabolic modelling/Matlab files scripts/Recon3DModel_301.mat, Metabolic modelling/Matlab files scripts/Similarity_index_script.mlx, Metabolic modelling/Matlab files scripts/modelMUT309.mat, Metabolic modelling/Matlab files scripts/modelWT39.mat, Metabolic modelling/Matlab files scripts/modelWT68.mat, Metabolic modelling/Matlab files scripts/Similarity_indexMUTvsCTRLs.mat, Metabolic modelling/Matlab files scripts/Similarity_index_all10comparisons.mat, Metabolic modelling/Matlab files scripts/model_generation22102021.mat, Metabolic modelling/Matlab files scripts/Similarity index Ali/model_1.mat, Metabolic modelling/Matlab files scripts/Similarity index Ali/model_2.mat, Metabolic modelling/Matlab files scripts/Similarity index Ali/similarity+part2.mat, Metabolic modelling/Matlab files scripts/Similarity index Ali/Calculate_FVA_Similarity_Example.m, Metabolic modelling/Matlab files scripts/Similarity index Ali/FVA_similarity_Thomas.m, Metabolic modelling/Matlab files scripts/Similarity index Ali/similarity_part2.mat, Metabolic modelling/R files scripts/Data_prep_for_fastcormics2.Rmd, Metabolic modelling/R files scripts/Similarity_bubble_charts.Rmd, Metabolic modelling/R files scripts/Variables_Data_prep_for_fastcormics2.RData
Update Image analysis quantification/FOXA2_TUJ1_TH_RS_1/distmatrix.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/f_barMask.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/f_CV8000_getChannelInfo.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/f_imageAnalysis.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/f_LogDependenciesLinux.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/f_LPF_by_FFT.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/FillEulerLUT.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/imoverlay2.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/Iris_GetOrganoidFields.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/Main.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/p_EulerInv.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/p_is_simple.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/p_oct_label.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/pk_follow_link.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/pk_get_nh.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/pk_get_nh_idx.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/Skel2Graph3D.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_1/Skeleton3D.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/distmatrix.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/f_barMask.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/f_CV8000_getChannelInfo.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/f_imageAnalysis.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/f_LogDependenciesLinux.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/f_LPF_by_FFT.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/FillEulerLUT.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/imoverlay2.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/Iris_GetOrganoidFields.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/Main.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/p_EulerInv.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/p_is_simple.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/p_oct_label.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/pk_follow_link.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/pk_get_nh.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/pk_get_nh_idx.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/Skel2Graph3D.m, Image analysis quantification/FOXA2_TUJ1_TH_RS_2/Skeleton3D.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/distmatrix.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/f_barMask.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/f_CV8000_getChannelInfo.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/f_imageAnalysis.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/f_LogDependenciesLinux.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/f_LPF_by_FFT.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/imoverlay2.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/Iris_GetOrganoidFields.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_1/Main.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/distmatrix.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/f_barMask.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/f_CV8000_getChannelInfo.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/f_imageAnalysis.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/f_LogDependenciesLinux.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/f_LPF_by_FFT.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/imoverlay2.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/Iris_GetOrganoidFields.m, Image analysis quantification/Ki67_Sox2_MAP2_RS_2/Main.m, Image analysis quantification/LAMP1_GCase_MAP2-Analysis/488LAMP1_568GCase_647MAP2_ZeissConfocal.m, Image analysis quantification/MAP2_S100b_GFAP_RS/distmatrix.m, Image analysis quantification/MAP2_S100b_GFAP_RS/f_barMask.m, Image analysis quantification/MAP2_S100b_GFAP_RS/f_CV8000_getChannelInfo.m, Image analysis quantification/MAP2_S100b_GFAP_RS/f_imageAnalysis.m, Image analysis quantification/MAP2_S100b_GFAP_RS/f_LogDependenciesLinux.m, Image analysis quantification/MAP2_S100b_GFAP_RS/f_LPF_by_FFT.m, Image analysis quantification/MAP2_S100b_GFAP_RS/FillEulerLUT.m, Image analysis quantification/MAP2_S100b_GFAP_RS/imoverlay2.m, Image analysis quantification/MAP2_S100b_GFAP_RS/Iris_GetOrganoidFields.m, Image analysis quantification/MAP2_S100b_GFAP_RS/Main.m, Image analysis quantification/MAP2_S100b_GFAP_RS/p_EulerInv.m, Image analysis quantification/MAP2_S100b_GFAP_RS/p_is_simple.m, Image analysis quantification/MAP2_S100b_GFAP_RS/p_oct_label.m, Image analysis quantification/MAP2_S100b_GFAP_RS/pk_follow_link.m, Image analysis quantification/MAP2_S100b_GFAP_RS/pk_get_nh.m, Image analysis quantification/MAP2_S100b_GFAP_RS/pk_get_nh_idx.m, Image analysis quantification/MAP2_S100b_GFAP_RS/Skel2Graph3D.m, Image analysis quantification/MAP2_S100b_GFAP_RS/Skeleton3D.m, Image analysis quantification/MAP2_TUJ1_TH_RS/distmatrix.m, Image analysis quantification/MAP2_TUJ1_TH_RS/f_barMask.m, Image analysis quantification/MAP2_TUJ1_TH_RS/f_CV8000_getChannelInfo.m, Image analysis quantification/MAP2_TUJ1_TH_RS/f_imageAnalysis.m, Image analysis quantification/MAP2_TUJ1_TH_RS/f_LogDependenciesLinux.m, Image analysis quantification/MAP2_TUJ1_TH_RS/f_LPF_by_FFT.m, Image analysis quantification/MAP2_TUJ1_TH_RS/FillEulerLUT.m, Image analysis quantification/MAP2_TUJ1_TH_RS/imoverlay2.m, Image analysis quantification/MAP2_TUJ1_TH_RS/Iris_GetOrganoidFields.m, Image analysis quantification/MAP2_TUJ1_TH_RS/Main.m, Image analysis quantification/MAP2_TUJ1_TH_RS/p_EulerInv.m, Image analysis quantification/MAP2_TUJ1_TH_RS/p_is_simple.m, Image analysis quantification/MAP2_TUJ1_TH_RS/p_oct_label.m, Image analysis quantification/MAP2_TUJ1_TH_RS/pk_follow_link.m, Image analysis quantification/MAP2_TUJ1_TH_RS/pk_get_nh.m, Image analysis quantification/MAP2_TUJ1_TH_RS/pk_get_nh_idx.m, Image analysis quantification/MAP2_TUJ1_TH_RS/Skel2Graph3D.m, Image analysis quantification/MAP2_TUJ1_TH_RS/Skeleton3D.m, Image analysis quantification/Nestin_Sox2_DCX_RS/distmatrix.m, Image analysis quantification/Nestin_Sox2_DCX_RS/f_barMask.m, Image analysis quantification/Nestin_Sox2_DCX_RS/f_CV8000_getChannelInfo.m, Image analysis quantification/Nestin_Sox2_DCX_RS/f_imageAnalysis.m, Image analysis quantification/Nestin_Sox2_DCX_RS/f_LogDependenciesLinux.m, Image analysis quantification/Nestin_Sox2_DCX_RS/f_LPF_by_FFT.m, Image analysis quantification/Nestin_Sox2_DCX_RS/FillEulerLUT.m, Image analysis quantification/Nestin_Sox2_DCX_RS/imoverlay2.m, Image analysis quantification/Nestin_Sox2_DCX_RS/Iris_GetOrganoidFields.m, Image analysis quantification/Nestin_Sox2_DCX_RS/Main.m, Image analysis quantification/Nestin_Sox2_DCX_RS/p_EulerInv.m, Image analysis quantification/Nestin_Sox2_DCX_RS/p_is_simple.m, Image analysis quantification/Nestin_Sox2_DCX_RS/p_oct_label.m, Image analysis quantification/Nestin_Sox2_DCX_RS/pk_follow_link.m, Image analysis quantification/Nestin_Sox2_DCX_RS/pk_get_nh.m, Image analysis quantification/Nestin_Sox2_DCX_RS/pk_get_nh_idx.m, Image analysis quantification/Nestin_Sox2_DCX_RS/Skel2Graph3D.m, Image analysis quantification/Nestin_Sox2_DCX_RS/Skeleton3D.m, Image analysis quantification/TH_DCX_MAP2_RS/distmatrix.m, Image analysis quantification/TH_DCX_MAP2_RS/f_barMask.m, Image analysis quantification/TH_DCX_MAP2_RS/f_CV8000_getChannelInfo.m, Image analysis quantification/TH_DCX_MAP2_RS/f_imageAnalysis.m, Image analysis quantification/TH_DCX_MAP2_RS/f_LogDependenciesLinux.m, Image analysis quantification/TH_DCX_MAP2_RS/f_LPF_by_FFT.m, Image analysis quantification/TH_DCX_MAP2_RS/FillEulerLUT.m, Image analysis quantification/TH_DCX_MAP2_RS/imoverlay2.m, Image analysis quantification/TH_DCX_MAP2_RS/Iris_GetOrganoidFields.m, Image analysis quantification/TH_DCX_MAP2_RS/Main.m, Image analysis quantification/TH_DCX_MAP2_RS/p_EulerInv.m, Image analysis quantification/TH_DCX_MAP2_RS/p_is_simple.m, Image analysis quantification/TH_DCX_MAP2_RS/p_oct_label.m, Image analysis quantification/TH_DCX_MAP2_RS/pk_follow_link.m, Image analysis quantification/TH_DCX_MAP2_RS/pk_get_nh.m, Image analysis quantification/TH_DCX_MAP2_RS/pk_get_nh_idx.m, Image analysis quantification/TH_DCX_MAP2_RS/Skel2Graph3D.m, Image analysis quantification/TH_DCX_MAP2_RS/Skeleton3D.m, Image analysis quantification/TH_Sox2_MAP2_RS/distmatrix.m, Image analysis quantification/TH_Sox2_MAP2_RS/f_barMask.m, Image analysis quantification/TH_Sox2_MAP2_RS/f_CV8000_getChannelInfo.m, Image analysis quantification/TH_Sox2_MAP2_RS/f_imageAnalysis.m, Image analysis quantification/TH_Sox2_MAP2_RS/f_LogDependenciesLinux.m, Image analysis quantification/TH_Sox2_MAP2_RS/f_LPF_by_FFT.m, Image analysis quantification/TH_Sox2_MAP2_RS/FillEulerLUT.m, Image analysis quantification/TH_Sox2_MAP2_RS/imoverlay2.m, Image analysis quantification/TH_Sox2_MAP2_RS/Iris_GetOrganoidFields.m, Image analysis quantification/TH_Sox2_MAP2_RS/Main.m, Image analysis quantification/TH_Sox2_MAP2_RS/p_EulerInv.m, Image analysis quantification/TH_Sox2_MAP2_RS/p_is_simple.m, Image analysis quantification/TH_Sox2_MAP2_RS/p_oct_label.m, Image analysis quantification/TH_Sox2_MAP2_RS/pk_follow_link.m, Image analysis quantification/TH_Sox2_MAP2_RS/pk_get_nh.m, Image analysis quantification/TH_Sox2_MAP2_RS/pk_get_nh_idx.m, Image analysis quantification/TH_Sox2_MAP2_RS/Skel2Graph3D.m, Image analysis quantification/TH_Sox2_MAP2_RS/Skeleton3D.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/Copy_of_f_imageAnalysis.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/Copy_of_Main.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/distmatrix.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/f_barMask.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/f_CV8000_getChannelInfo.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/f_imageAnalysis.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/f_LogDependenciesLinux.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/f_LPF_by_FFT.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/imoverlay2.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/Iris_GetOrganoidFields.m, Image analysis quantification/TUJ1_LMNB1_Sox2-RS_1/Main.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/distmatrix.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/f_barMask.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/f_CV8000_getChannelInfo.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/f_imageAnalysis.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/f_LogDependenciesLinux.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/f_LPF_by_FFT.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/imoverlay2.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/Iris_GetOrganoidFields.m, Image analysis quantification/TUJ1_LMNB1_Sox2_RS_2/Main.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/distmatrix.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/f_barMask.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/f_CV8000_getChannelInfo.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/f_imageAnalysis.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/f_LogDependenciesLinux.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/f_LPF_by_FFT.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/imoverlay2.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/Iris_GetOrganoidFields.m, Image analysis quantification/pSyn_TotSyn_MAP2_RS/Main.m
Update Data processing and plotting/Figure 1B - GCase activity/Environment.RData, Data processing and plotting/Figure 1B - GCase activity/GCase.Rmd, Data processing and plotting/Figure 1B - GCase activity/GCase.nb.html, Data processing and plotting/Figure 4A - DA ELISA/DA ELISA plots.nb.html, Data processing and plotting/Figure 4A - DA ELISA/DA ELISA plots.Rmd, Data processing and plotting/Figure 5A - DA genes/Environment.RData, Data processing and plotting/Figure 5A - DA genes/DA differentiation genes.Rmd, Data processing and plotting/Figure 5G - PI staining_Cell cycle plotting/Environment.RData, Data processing and plotting/Figure 5G - PI staining_Cell cycle plotting/PI staining.Rmd, Data processing and plotting/Figure 5G - PI staining_Cell cycle plotting/PI staining.nb.html, Data processing and plotting/Figure S3D - Seahorse/Environment.RData, Data processing and plotting/Figure S3D - Seahorse/Plots Seahorse.Rmd, Data processing and plotting/Figure S4D - PI signaling genes/Environment.RData, Data processing and plotting/Figure S4D - PI signaling genes/PI signaling genes.Rmd, Data processing and plotting/Figure S7C - OrganoidSize/Environment.RData, Data processing and plotting/Figure S7C - OrganoidSize/Plots_OrganoidSize.Rmd, Data processing and plotting/Image analysis data processing and plotting/Environment.RData, Data processing and plotting/Image analysis data processing and plotting/Stainings.Rmd, Data processing and plotting/Image analysis data processing and plotting/Stainings.nb.html, Data processing and plotting/Image analysis data processing and plotting/Figure 5L - LaminB1 staining/Environment.RData, Data processing and plotting/Image analysis data processing and plotting/Figure 5L - LaminB1 staining/LMNB1 stainings.Rmd, Data processing and plotting/WB data processing and plotting/Environment.RData, Data processing and plotting/WB data processing and plotting/WB data processing and plotting.nb.html, Data processing and plotting/WB data processing and plotting/WB data processing and plotting.Rmd
Update Data processing and plotting/Enrichment analysis plotting/Environment.RData, Data processing and plotting/Enrichment analysis plotting/Visualization_of_enrichment_analysis_.Rmd
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