polCAs

Polarized cortical assembloids (polCAs)

Here the code used to analyse polCAs Single Cell data

base docker image can be retrieved via docker pull testalab/downstream:polaroid-0.1.3

list of additional libraries installed locally can be found in data/env/python3_libs.txt and data/env/R_libs.txt

Data should be placed as follows:

Anndata of Badhuri et. al (10.1038/s41586-021-03910-8) ./data/Badhuri_atlas.h5ad

Ppoliudakis et. al(10.1016/j.neuron.2019.06.011): ./data/Geschwind_atlas.h5ad

Raw data of experiments (control1_piece1, control1_piece2 ... polaroid3_distal): ./data

or pre-processed polCAs (optional): ./outdir/02C_Preprocess_final.h5ad

An html version of the notebooks is accessible here.

Name		Name	Last commit message	Last commit date
Latest commit History 47 Commits
.github/workflows		.github/workflows
data		data
figures		figures
outdir		outdir
resources		resources
.gitignore		.gitignore
Badhuri0.Preprocess.ipynb		Badhuri0.Preprocess.ipynb
Badhuri01B.ProgenitorsReanalysis.ipynb		Badhuri01B.ProgenitorsReanalysis.ipynb
Badhuri01C.CyclingReanalysis.ipynb		Badhuri01C.CyclingReanalysis.ipynb
Badhuri02.preBulk.ipynb		Badhuri02.preBulk.ipynb
Badhuri02B.pseudoBulking.ipynb		Badhuri02B.pseudoBulking.ipynb
Badhuri03A_Neurons.3pointsModel.pBulk_byArea_scaling.ipynb		Badhuri03A_Neurons.3pointsModel.pBulk_byArea_scaling.ipynb
Badhuri03B_Progenitors.3pointsModel.pBulk_byArea_scaling.ipynb		Badhuri03B_Progenitors.3pointsModel.pBulk_byArea_scaling.ipynb
Badhuri03C_Cycling.3pointsModel.pBulk_byArea_scaling.ipynb		Badhuri03C_Cycling.3pointsModel.pBulk_byArea_scaling.ipynb
BraunAtlas_comparison.01atlasPrep.ipynb		BraunAtlas_comparison.01atlasPrep.ipynb
BraunAtlas_comparison.02organopidsPrep.ipynb		BraunAtlas_comparison.02organopidsPrep.ipynb
BraunAtlas_comparison.03polCAsCompare.ipynb		BraunAtlas_comparison.03polCAsCompare.ipynb
BraunAtlas_comparison.04KantonCompare.ipynb		BraunAtlas_comparison.04KantonCompare.ipynb
BraunAtlas_comparison.05VelascoCompare.ipynb		BraunAtlas_comparison.05VelascoCompare.ipynb
COL1A2genes.ipynb		COL1A2genes.ipynb
LICENSE.txt		LICENSE.txt
MfuzzTrends.ipynb		MfuzzTrends.ipynb
README.md		README.md
colorMap.yaml		colorMap.yaml
harmony_mod.py		harmony_mod.py
polCAs01_RawImport.ipynb		polCAs01_RawImport.ipynb
polCAs02_Preprocess_Gruffi.ipynb		polCAs02_Preprocess_Gruffi.ipynb
polCAs03_Dimreduct_exploration.ipynb		polCAs03_Dimreduct_exploration.ipynb
polCAs04.2_Differential_abundance.ipynb		polCAs04.2_Differential_abundance.ipynb
polCAs04_Dimreduct_inDepthMarkers.ipynb		polCAs04_Dimreduct_inDepthMarkers.ipynb
polCAs05_RG_and_Neurons_Focus.ipynb		polCAs05_RG_and_Neurons_Focus.ipynb
polCAs06_Dimreduct_inDepthCompositions.ipynb		polCAs06_Dimreduct_inDepthCompositions.ipynb
polCAs08_Developmental_Trajectories.ipynb		polCAs08_Developmental_Trajectories.ipynb
polCAsBadhuriSpace_LoadingsAgreementBarplot.ipynb		polCAsBadhuriSpace_LoadingsAgreementBarplot.ipynb
polCAsCycling01_Selection.ipynb		polCAsCycling01_Selection.ipynb
polCAsCycling02_pBulk.ipynb		polCAsCycling02_pBulk.ipynb
polCAsCycling03_fg8_tomato_check.ipynb		polCAsCycling03_fg8_tomato_check.ipynb
polCAsCycling04_pBulk_bySegment.DEA.ipynb		polCAsCycling04_pBulk_bySegment.DEA.ipynb
polCAsCycling05A_POLAROIDS_BadhuriSpace.ipynb		polCAsCycling05A_POLAROIDS_BadhuriSpace.ipynb
polCAsCycling05B_CONTROLS_BadhuriSpace.ipynb		polCAsCycling05B_CONTROLS_BadhuriSpace.ipynb
polCAsCycling05C_ALL_BadhuriSpace.ipynb		polCAsCycling05C_ALL_BadhuriSpace.ipynb
polCAsNeurons01_Selection.ipynb		polCAsNeurons01_Selection.ipynb
polCAsNeurons02_pBulk.ipynb		polCAsNeurons02_pBulk.ipynb
polCAsNeurons03_fg8_tomato_check.ipynb		polCAsNeurons03_fg8_tomato_check.ipynb
polCAsNeurons04_pBulk_bySegment.DEA.ipynb		polCAsNeurons04_pBulk_bySegment.DEA.ipynb
polCAsNeurons05A_POLAROIDS_BadhuriSpace.ipynb		polCAsNeurons05A_POLAROIDS_BadhuriSpace.ipynb
polCAsNeurons05B_CONTROLS_BadhuriSpace.ipynb		polCAsNeurons05B_CONTROLS_BadhuriSpace.ipynb
polCAsNeurons05C_ALL_BadhuriSpace.ipynb		polCAsNeurons05C_ALL_BadhuriSpace.ipynb
polCAsProgenitors01_Selection.ipynb		polCAsProgenitors01_Selection.ipynb
polCAsProgenitors02_pBulk.ipynb		polCAsProgenitors02_pBulk.ipynb
polCAsProgenitors03_fg8_tomato_check.ipynb		polCAsProgenitors03_fg8_tomato_check.ipynb
polCAsProgenitors04_pBulk_bySegment.DEA.ipynb		polCAsProgenitors04_pBulk_bySegment.DEA.ipynb
polCAsProgenitors05A_POLAROIDSBadhuriSpace.ipynb		polCAsProgenitors05A_POLAROIDSBadhuriSpace.ipynb
polCAsProgenitors05B_CONTROLS_BadhuriSpace.ipynb		polCAsProgenitors05B_CONTROLS_BadhuriSpace.ipynb
polCAsProgenitors05C_ALL_BadhuriSpace.ipynb		polCAsProgenitors05C_ALL_BadhuriSpace.ipynb

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polCAs

Badhuri0.Preprocess

Badhuri01B.ProgenitorsReanalysis

Badhuri01C.CyclingReanalysis

Badhuri02.preBulk

Badhuri02B.pseudoBulking

Badhuri03A_Neurons.3pointsModel

Badhuri03B_Progenitors.3pointsModel

Badhuri03C_Cycling.3pointsModel

polCAs01_RawImport

polCAs02_Preprocess_Gruffi

polCAs03_Dimreduct_exploration

polCAs04_Dimreduct_inDepthMarkers

polCAs04.2_Differential_abundance

polCAs05_RG_and_Neurons_Focus

polCAs06_Dimreduct_inDepthCompositions

polCAs08_Developmental_Trajectories

polCAsCycling01_Selection

polCAsCycling02_pBulk

polCAsCycling03_fg8_tomato_check

polCAsCycling04_pBulk_bySegment.DEA

polCAsCycling05A_POLAROIDS_BadhuriSpace

polCAsCycling05B_CONTROLS_BadhuriSpace

polCAsCycling05C_ALL_BadhuriSpace

polCAsBadhuriSpace_LoadingsAgreement

polCAsProgenitors01_Selection

polCAsProgenitors02_pBulk

polCAsProgenitors03_fg8_tomato_check

polCAsProgenitors04_pBulk_bySegment.DEA

polCAsProgenitors05A_POLAROIDSBadhuriSpace

polCAsProgenitors05B_CONTROLS_BadhuriSpace

polCAsProgenitors05C_ALL_BadhuriSpace

polCAsNeurons01_Selection

polCAsNeurons02_pBulk

polCAsNeurons03_fg8_tomato_check

polCAsNeurons04_pBulk_bySegment.DEA

polCAsNeurons05A_POLAROIDS_BadhuriSpace

polCAsNeurons05B_CONTROLS_BadhuriSpace

polCAsNeurons05C_ALL_BadhuriSpace

MfuzzTrends

BraunAtlas_comparison_01atlasPrep

BraunAtlas_comparison_02organopidsPrep

BraunAtlas_comparison_03polCAsCompare

BraunAtlas_comparison_04KantonCompare

BraunAtlas_comparison_05VelascoCompare

COL1A2gene_check

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