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
*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