Last updated: 2020-10-19

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Knit directory: Embryoid_Body_Pilot_Workflowr/analysis/

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Rmd 87c7292 KLRhodes 2020-08-04 Start workflowr project.

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

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

*Filtering and Normalizing each 10x lane + Batch1Lane1
+ Batch1Lane3
+ Batch1Lane4
+ Batch1Lane5
+ Batch1Lane6
+ Batch1Lane7
+ Batch1Lane8
+ Batch1Lane9
+ Batch2Lane1
+ Batch2Lane2
+ Batch2Lane3
+ Batch2Lane4
+ Batch3Lane1
+ Batch3Lane2
+ Batch3Lane3
+ Batch3Lane4

*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