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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, spheroids 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 {.tabset}
##1. Run EmptyDrops, Add Metadata to Seurat object from each 10x lane
##2. Filter and run SCTransform on each 10x lane {.tabset-dropdown}
-[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 {.tabset}{.tabset-dropdown}
[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)