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4 changes: 2 additions & 2 deletions README.md
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**For current up to date scATAC-seq analysis https://github.com/GreenleafLab/ArchR**

**scATAC_01** - Script for reading in 10x scATAC-seq fragments identify cells using number of fragments and TSS enrichment scores and saving fitlered fragments.
**scATAC_01** - Script for reading in 10x scATAC-seq fragments identify cells using number of fragments and TSS enrichment scores and saving filtered fragments.

**scATAC_02** - Script for pre-clustering using large windows genome-wide and then calling peaks on putative clusters and create a master peak set

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## Integration (scATAC + scRNA) Analyses

**scRNA_scATAC_Integration_01** - Alignment of scRNA and scATAC-seq data using Seurat CCA and identifcation of nearest
**scRNA_scATAC_Integration_01** - Alignment of scRNA and scATAC-seq data using Seurat CCA and identification of nearest
neighbors across modalities.

**scRNA_scATAC_Integration_02** - Aggregate scRNA + scATAC-seq data for correlation focused analysis.
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