Scripts for Analysis

Scripts used for analysis of V1 and V2 Datasets.
seurat_v1.R - initialize seurat object from 10X Genomics cellranger outputs. Includes filtering, normalization, regression, variable gene identification, PCA analysis, clustering, tSNE visualization. Used for v1 datasets.
merge_seurat.R - merge two or more seurat objects into one seurat object. Perform linear regression to remove batch effects from separate objects. Used for v1 datasets.
subcluster_seurat_v1.R - subcluster clusters of interest from Seurat object. Determine variable genes, perform regression and PCA. Used for v1 datasets.
seurat_v2.R - initialize seurat object from 10X Genomics cellranger outputs. Includes filtering, normalization, regression, variable gene identification, and PCA analysis. Used for v2 datasets.
clustering_markers_v2.R - clustering and tSNE visualization for v2 datasets.
subcluster_seurat_v2.R - subcluster clusters of interest from Seurat object. Determine variable genes, perform regression and PCA analysis. Used for v2 datasets.
seurat_object_analysis_v1_and_v2.R - downstream analysis and plotting functions for seurat object created by seurat_v1.R or seurat_v2.R.
merge_clusters.R - merge clusters that do not meet gene threshold. Used for both v1 and v2 datasets.
prepare_for_monocle_v1.R - subcluster cells of interest and perform linear regression, but not scaling in order to input normalized, regressed values into monocle with monocle_seurat_input_v1.R
monocle_seurat_input_v1.R - monocle script using seurat batch corrected values as input for v1 merged timecourse datasets.
monocle_lineage_trace.R - monocle script using nUMI as input for v2 lineage traced dataset.
monocle_object_analysis.R - downstream analysis for monocle object - BEAM and plotting.
CCA_merging_v2.R - script for merging v2 endocrine datasets with canonical correlation analysis and determining the number of CCs to include in downstream analysis.
CCA_alignment_v2.R - script for downstream alignment, clustering, tSNE visualization, and differential gene expression analysis.