hEGCLC paper
Repository to collect the code used to analyze the scRNA-Seq and DNA methylation data for the paper ()[]
Docker image for most of the single cell analysis (notebooks in folders from 00 to 05) can be retrieved via docker pull alessiavalenti/transgenerationalhub:transgenerational-1.1.7.
00_ExplorationQC_DimRed_Clustering.ipynb
First exploration, quality check, dimensionality reduction and clustering of the scRNA-Seq data.
01a_CellsAnnotationMarkers.ipynb
Exploration of known markers across clusters of the scRNA-Seq data and cell types annotation.
01b_FunctionalEnrichment_Clusters.ipynb
Functional enrichment of the markers of the Leiden clusters.
01c_CellCycle.ipynb
Analysis of cell cycle phases of the cells in the scRNA-Seq data.
02a_PseudoBulk_PCA.ipynb
Generation of pseudobulk from annotated scRNA-Seq and PCA analysis.
02b_Pseudobulk_edgeR_topGO_hEGCLC_hPGCLC.ipynb
Differential expression analysis and functional enrichment of DEGs from pseudobulks of hPGCLC and hEGCLC.
02b_Pseudobulk_edgeR_topGO_hiPSC_hEGCLC.ipynb
Differential expression analysis and functional enrichment of DEGs from pseudobulks of hiPSC and hEGCLC.
02b_Pseudobulk_edgeR_topGO_hiPSC_hPGCLC.ipynb
Differential expression analysis and functional enrichment of DEGs from pseudobulks of hPGCLC and hiPSC.
02c_Comparisons_between_DEGs.ipynb
Comparison of DEGs of comparisons hPGCLC-hEGCLC, hiPSC-hEGCLC and hPGCLC-hiPSC.
03a_Chen_Processing_and_Annotation.ipynb
Processing of dataset from Chen et al. (Cell Reports, 2019) and annotation of the cell types.
03b_Ingest_Chen.ipynb
Ingestion of in-house dataset onto Chen dataset.
03c_Fetal_Processing_and_Annotation.ipynb
Processing of dataset from Chen et al. (Cell Reports, 2019) and annotation of the cell types.
03d_Ingest_FetalData.ipynb
Processing of dataset from Guo et al. (Cell Reports, 2019) and annotation of the cell types.
04a_DEGs_patterns_AggClustering.ipynb
Clustering of genes based on the logFC patterns along the hiPSC-iMeLC-hPGCLC-hEGCLC axis.
05_TF_activity_inference.ipynb
Inference of TF activity from scRNA-Seq data using Multivariate Linear Model.
FuncEnrich_LeidenCluster_0
Functional enrichment of Leiden cluster 0 from clustering in notebook 01
FuncEnrich_LeidenCluster_1
Functional enrichment of Leiden cluster 1 from clustering in notebook 01
FuncEnrich_LeidenCluster_2
Functional enrichment of Leiden cluster 2 from clustering in notebook 01
FuncEnrich_LeidenCluster_3
Functional enrichment of Leiden cluster 3 from clustering in notebook 01
FuncEnrich_LeidenCluster_4
Functional enrichment of Leiden cluster 4 from clustering in notebook 01
FuncEnrich_LeidenCluster_5
Functional enrichment of Leiden cluster 5 from clustering in notebook 01
FuncEnrich_LeidenCluster_6
Functional enrichment of Leiden cluster 6 from clustering in notebook 01
FuncEnrich_LeidenCluster_7
Functional enrichment of Leiden cluster 7 from clustering in notebook 01
FuncEnrich_LeidenCluster_8
Functional enrichment of Leiden cluster 8 from clustering in notebook 01
FuncEnrich_LeidenCluster_9
Functional enrichment of Leiden cluster 9 from clustering in notebook 01
FuncEnrich_LeidenCluster_10
Functional enrichment of Leiden cluster 10 from clustering in notebook 01
FuncEnrich_LeidenCluster_11
Functional enrichment of Leiden cluster 11 from clustering in notebook 01
FuncEnrich_LeidenCluster_12
Functional enrichment of Leiden cluster 12 from clustering in notebook 01
FuncEnrich_GenesCluster_0
Functional enrichment of genes in cluster 0 from clustering in notebook 04a
FuncEnrich_GenesCluster_1
Functional enrichment of genes in cluster 1 from clustering in notebook 04a
FuncEnrich_GenesCluster_2
Functional enrichment of genes in cluster 2 from clustering in notebook 04a
FuncEnrich_GenesCluster_3
Functional enrichment of genes in cluster 3 from clustering in notebook 04a
FuncEnrich_GenesCluster_4
Functional enrichment of genes in cluster 4 from clustering in notebook 04a
FuncEnrich_GenesCluster_5
Functional enrichment of genes in cluster 5 from clustering in notebook 04a
FuncEnrich_GenesCluster_6
Functional enrichment of genes in cluster 6 from clustering in notebook 04a
FuncEnrich_GenesCluster_7
Functional enrichment of genes in cluster 7 from clustering in notebook 04a
FuncEnrich_GenesCluster_8
Functional enrichment of genes in cluster 8 from clustering in notebook 04a
FuncEnrich_GenesCluster_9
Functional enrichment of genes in cluster 9 from clustering in notebook 04a
FuncEnrich_GenesCluster_10
Functional enrichment of genes in cluster 10 from clustering in notebook 04a
FuncEnrich_GenesCluster_11
Functional enrichment of genes in cluster 11 from clustering in notebook 04a
FuncEnrich_GenesCluster_12
Functional enrichment of genes in cluster 12 from clustering in notebook 04a
FuncEnrich_GenesCluster_13
Functional enrichment of genes in cluster 13 from clustering in notebook 04a
FuncEnrich_GenesCluster_14
Functional enrichment of genes in cluster 14 from clustering in notebook 04a