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index.Rmd
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index.Rmd
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---
title: "Home"
site: workflowr::wflow_site
output:
workflowr::wflow_html:
toc: true
toc_depth: 1
editor_options:
chunk_output_type: console
---
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
+ [Batch1Lane1](SampleFilteringandSCT_Batch1Lane1.html)
+ [Batch1Lane3](SampleFilteringandSCT_Batch1Lane3.html)
+ [Batch1Lane4](SampleFilteringandSCT_Batch1Lane4.html)
+ [Batch1Lane5](SampleFilteringandSCT_Batch1Lane5.html)
+ [Batch1Lane6](SampleFilteringandSCT_Batch1Lane6.html)
+ [Batch1Lane7](SampleFilteringandSCT_Batch1Lane7.html)
+ [Batch1Lane8](SampleFilteringandSCT_Batch1Lane8.html)
+ [Batch1Lane9](SampleFilteringandSCT_Batch1Lane9.html)
+ [Batch2Lane1](SampleFilteringandSCT_Batch2Lane1.html)
+ [Batch2Lane2](SampleFilteringandSCT_Batch2Lane2.html)
+ [Batch2Lane3](SampleFilteringandSCT_Batch2Lane3.html)
+ [Batch2Lane4](SampleFilteringandSCT_Batch2Lane4.html)
+ [Batch3Lane1](SampleFilteringandSCT_Batch3Lane1.html)
+ [Batch3Lane2](SampleFilteringandSCT_Batch3Lane2.html)
+ [Batch3Lane3](SampleFilteringandSCT_Batch3Lane3.html)
+ [Batch3Lane4](SampleFilteringandSCT_Batch3Lane4.html)
# Merging and integration, seurat clustering
+ [Harmony correcting for Batch](IntegrateAnalysis.afterFilter.HarmonyBatch.html)
+ [Harmony correcting for Batch, Individual](IntegrateAnalysis.afterFilter.HarmonyBatchindividual.html)
+ [Harmony correcting for Batch, Individual, and Lane](IntegrateAnalysis.afterFilter.HarmonyBatchSampleIDindividual.html)
+ [SCTransform regressing out Batch,individual](IntegrateAnalysis.afterFilter.SCTregressBatchIndividual.html)
+ [SCTransform regressing out Batch,individual then Harmony correcting batch and individual](IntegrateAnalysis.afterFilter.SCTregressBatchIndividualHarmonyBatchindividual.html)
+ [No Integration, Just Merged](IntegrateAnalysis.afterFilter.NOHARMONYjustmerge.html)
Note: all analyses below use data corrected using Haromy for Batch and Individual
# Differential Expression with limma (Pseudobulk)
+ [Using Cluster Resolution 0.1](Pseudobulk_Limma_Harmony.BatchIndividual_ClusterRes0.1_minPCT0.2.Rmd)
+ [Using Cluster Resolution 0.5](Pseudobulk_Limma_Harmony.BatchIndividual_ClusterRes0.5_minPCT0.2.Rmd)
# Seurat subclustering
+ To be added soon!
# Cell type identification using scHCL
+ [scHCL analysis](RunscHCL_HarmonyBatchInd.Rmd)
# Topic Modelling with FastTopics
+ to be added soon!
#Hierachical clustering of gene expression
+ [Single Cell Resolution](SingleCell_HierarchicalClustering_NoGeneFilter.Rmd)
+ [Pseudobulk, Using Cluster Resolution 0.1](Pseudobulk_HierarchicalClustering_Harmony.Batchindividual_ClusterRes0.1_minPCT0.2.Rmd)
+ [Pseudobulk, Using Cluster Resolution 0.5](Pseudobulk_HierarchicalClustering_Harmony.Batchindividual_ClusterRes0.5_minPCT0.2.Rmd)
+ [Pseudobulk, Using Cluster Resolution 0.8](Pseudobulk_HierarchicalClustering_Harmony.Batchindividual_ClusterRes0.8_minPCT0.2.Rmd)
+ [Pseudobulk, Using Cluster Resolution 1](Pseudobulk_HierarchicalClustering_Harmony.Batchindividual_ClusterRes1_minPCT0.2.Rmd)
# Variance Partition (to determine the relative contribution of Cluster, Batch, and Individual to variation in gene expression)
+ [Pseudobulk, Using Cluster Resolution 0.1](Pseudobulk_VariancePartition_Harmony.Batchindividual_ClusterRes0.1_minPCT0.2.Rmd)
+ [Pseudobulk, Using Cluster Resolution 0.5](Pseudobulk_VariancePartition_Harmony.Batchindividual_ClusterRes0.5_minPCT0.2.Rmd)
+ [Pseudobulk, Using Cluster Resolution 0.8](Pseudobulk_VariancePartition_Harmony.Batchindividual_ClusterRes0.8_minPCT0.2.Rmd)
+ [Pseudobulk, Using Cluster Resolution 1](Pseudobulk_VariancePartition_Harmony.Batchindividual_ClusterRes1_minPCT0.2.Rmd)
# Trajectory Inference with Scanpy/PAGA
+ to be added soon!
# Identification/Exploration of Dynamic Gene Module with Split-GPM
+ Link to Josh Popp's github to be added soon