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.gitignore
.gitignore
 
 
ArchR.qsub
ArchR.qsub
 
 
Custom_Peaks_To_Mutations.Rmd
Custom_Peaks_To_Mutations.Rmd
 
 
Figure1.png
Figure1.png
 
 
Non-Coding-Mutations-Multiome-Analysis.Rproj
Non-Coding-Mutations-Multiome-Analysis.Rproj
 
 
README.md
README.md
 
 
analysis_1.Rmd
analysis_1.Rmd
 
 
archR.Rmd
archR.Rmd
 
 
archR_workflow_script.R
archR_workflow_script.R
 
 
featureplot_atac_cd3e_cd79a.png
featureplot_atac_cd3e_cd79a.png
 
 
featureplot_rna_cd3e_cd79a.png
featureplot_rna_cd3e_cd79a.png
 
 
optimizeLSI.R
optimizeLSI.R
 
 
scATAC_01_Filter_Cells.R
scATAC_01_Filter_Cells.R
 
 
scATAC_02_Get_Peak_Set_hg19_v2.R
scATAC_02_Get_Peak_Set_hg19_v2.R
 
 
scATAC_03_Clustering_UMAP_v1.R
scATAC_03_Clustering_UMAP_v1.R
 
 
scATAC_04_Compute_Gene_Scores.R
scATAC_04_Compute_Gene_Scores.R
 
 
scATAC_05_Cluster_Disease_w_Reference_v1.R
scATAC_05_Cluster_Disease_w_Reference_v1.R
 
 
scATAC_seurat_1.Rmd
scATAC_seurat_1.Rmd
 
 
scRNA_01_Clustering_UMAP_v1.R
scRNA_01_Clustering_UMAP_v1.R
 
 
scRNA_02_Cluster_Disease_w_Reference_v1.R
scRNA_02_Cluster_Disease_w_Reference_v1.R
 
 
scRNA_scATAC_Integration_01_Align_scATAC_scRNA.R
scRNA_scATAC_Integration_01_Align_scATAC_scRNA.R
 
 
scRNA_scATAC_Integration_02_Create_Aggregate_scATAC_scRNA.R
scRNA_scATAC_Integration_02_Create_Aggregate_scATAC_scRNA.R
 
 
scRNA_scATAC_Integration_03_Compute_Peak_to_Gene_links.R
scRNA_scATAC_Integration_03_Compute_Peak_to_Gene_links.R
 
 
scRNA_scATAC_Integration_04_Link_TFs_To_Targets.R
scRNA_scATAC_Integration_04_Link_TFs_To_Targets.R
 
 
scRNA_workflow_custom.R
scRNA_workflow_custom.R
 
 
seurat_analysis.Rmd
seurat_analysis.Rmd
 
 

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