Last updated: 2020-10-19

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Knit directory: Embryoid_Body_Pilot_Workflowr/analysis/

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Welcome to my research website.

This site contains analyses performed on human Embryoid bodies, aggregates of spontaneously differentiating cells generated from induced pluripotent stem cells.

Single Cell RNA-seq data was collected using the 10x platform.

*Preprocessing, QC, and filtering +to be added soon!

*Run EmptyDrops, Add Metadata to Seurat object from each 10x lane
+to be added soon!

*Filtering and Normalizing each 10x lane

*Merging and integration, seurat clustering + Harmony correcting for Batch + Harmony correcting for Batch, Individual
+ Harmony correcting for Batch, Individual, and Lane
+ SCTransform regressing out Batch,individual
+ SCTransform regressing out Batch,individual then Harmony correcting batch and individual
+ No Integration, Just Merged

Note: all analyses below use data corrected using Haromy for Batch and Individual

*Differential Expression with limma (Pseudobulk) + Using Cluster Resolution 0.1 + Using Cluster Resolution 0.5

*Seurat subclustering + To be added soon!

*Cell type identification using scHCL + scHCL analysis

*Topic Modelling with FastTopics + to be added soon!

*Hierachical clustering of gene expression + Single Cell Resolution + Pseudobulk, Using Cluster Resolution 0.1 + Pseudobulk, Using Cluster Resolution 0.5 + Pseudobulk, Using Cluster Resolution 0.8 + Pseudobulk, Using Cluster Resolution 1

*Variance Partition (to determine the relative contribution of Cluster, Batch, and Individual to variation in gene expression) + Pseudobulk, Using Cluster Resolution 0.1 + Pseudobulk, Using Cluster Resolution 0.5 + Pseudobulk, Using Cluster Resolution 0.8 + Pseudobulk, Using Cluster Resolution 1