Organoid Multiplexing

This repo contains the code used to analyze Single cell data of organoid Multiplexing

Docker image for main analysis can be retrieved via docker pull testalab/downstream:organoidMultiplexing-1.1.0

After alignment of each sample, Cellranger's output: features, barcodes and count matrix should be placed in data/Sample*/filtered_feature_bc_matrix respective directories

Additional resources should be placed in data/resources.

genes.gtf (gex-GRCh38-2020-A gtf), KOLF2C1 wgs data from hipsci, single cell eqtl data from jerber et al. (https://doi.org/10.1038/s41588-021-00801-6)

In addition pipeline for consensus deconvolution can be found at https://github.com/GiuseppeTestaLab/demultiplexing-workflow

Finally VarAdata were generated using the SCanSNP version https://github.com/GiuseppeTestaLab/SCanSNP specifying --mode matrixgen

01_HVGs_joining.ipynb

01.1_Dataset_Preprocessing_DownD50.ipynb

01.2_Dataset_Preprocessing_UpD50.ipynb

01.3_Dataset_Preprocessing_DownD100.ipynb

01.4_Dataset_Preprocessing_UpD100_1.ipynb

01.5_Dataset_Preprocessing_UpD100_2.ipynb

01.6_Dataset_Preprocessing_DownD250.ipynb

01.7_Dataset_Preprocessing_UpD300.ipynb

02_Dataset_Merging.ipynb

03_Dataset_Not_Integrated_JointScale.ipynb

04_Dataset_Integration_Harmony.ipynb

05_Clusters_Annotation_All.ipynb

05.2_inGestion.ipynb

06_Exploration.ipynb

07_Paga.ipynb

08_DA.ipynb

08.0_Astrocytes_HVGs.ipynb

08.1_Astrocytes_Lineage.ipynb

09.0_Cajal_HVGs.ipynb

09.1_Cajal_Lineage.ipynb

10.0_Exc_HVGs.ipynb

10.1_Exc_Lineage.ipynb

11.0_Interneurons_HVGs.ipynb

11.1_Interneurons_Lineage.ipynb

12.0_MigratingNeurons_HVGs.ipynb

12.1_MigratingNeurons_Lineage.ipynb

13.0_varAnndata_prep_new.ipynb

13.1_SantyCheck.ipynb

13.2_ASE_explo.ipynb

15_Lines_Balance.ipynb

16_Tools_comparison.ipynb

17_Sample1_Benchmarking.ipynb

18_Sample2_Benchmarking.ipynb

19_BenchmarkingPlots.ipynb

20_QC_Filtering.ipynb

21_Integration.ipynb

22_CBO_VisualizationAndModelling.ipynb

23_PSC_VisualizationAndModelling.ipynb

24_CensusSeq.ipynb

25_CorrelateGrowths.ipynb

26_Recoverable_lines.ipynb

27_Scalability_comparison.ipynb