Single Cell Analysis of Epithelium, Spleen, and Pooled Tissue
Connor Eck
2025-09-19
library(readr)
library(knitr)
library(DT)
library(dplyr)Overview
Quality Control
Cells with mitochondrial counts above 5% and feature count below 200 were filtered out.
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Basic Stats
Summary Statistics
Table of Cell Counts Per Sample
Table of Cell Counts Per Cluster
Table of Cell Counts Per Cluster Filtered
Initial UMAP Clustering
UMAP clusters with no QC or batch correction.
UMAPS
UMAP Colored by TranscriptClick to expand figure
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Heatmap
Heatmap of Gene expression per cluster
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UMAP Clustering after QC
This section generates UMAP clustering after filtering out cells with greater than 5% mitochondrial gene counts and less than 200 features.
UMAP Colored by TranscriptClick to expand figure
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Heatmap
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UMAP Clustering after Batch Correction
This section generates UMAP clustering after filtering out cells with greater than 5% mitochondrial gene counts and less than 200 features. Batch correction is implemented with Harmony before clustering.
UMAP Colored by TranscriptClick to expand figure
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Heatmap
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UMAP Clustering with small K
UMAP clustering with max k = 8.
TODO
Gene heatmaps
List of Genes
Put list of genes in the dataset here
Look at TCR Beta+ CD4 T cells and subset
Differential Gene Expression
Compare across samples. Green spleen (861,863,864,865), Red Spleen (Pooled), Pooled JLN, Epithelium (861,863,864,865).
TCR
What clonotypes are enriched?
What clonotypes are enriched across samples?