diff --git a/R/GSE148946/DiabetesFibroblastGSE148946Nuclei.r b/R/GSE148946/DiabetesFibroblastGSE148946Nuclei.r
index 0400615..2eb5084 100644
--- a/R/GSE148946/DiabetesFibroblastGSE148946Nuclei.r
+++ b/R/GSE148946/DiabetesFibroblastGSE148946Nuclei.r
@@ -4,18 +4,22 @@ library(patchwork)
 library(clustifyr)
 library(tidyverse)
 
-mat_FibroblastNucleiDiabetes <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148946/suppl/GSE148946_wholecell_normdata.csv.gz")
+mat_FibroblastNucleiDiabetesExtraCol <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148946/suppl/GSE148946_wholecell_normdata.csv.gz")
+mat_FibroblastNucleiDiabetes = subset(mat_FibroblastNucleiDiabetesExtraCol, select = -c(gene_1))
 mat_FibroblastNucleiDiabetes <- mat_FibroblastNucleiDiabetes %>%
-  as.data.frame() %>%
-  column_to_rownames('gene') %>%
-  as.matrix() %>%
-  t()
+  #as.data.frame() %>%
+  column_to_rownames('gene')
+  #as.matrix() %>%
+  #t()
 mat_FibroblastNucleiDiabetes[1:5, 1:5]
 
 meta_FibroblastNucleiDiabetes <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148946/suppl/GSE148946_wholecell_metadata.csv.gz")
 sum(colnames(mat_FibroblastNucleiDiabetes) %in% meta_FibroblastNucleiDiabetes$orig.ident)
 ncol(mat_FibroblastNucleiDiabetes)
 
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_FibroblastNucleiDiabetes))
+
 new_ref_matrix <- average_clusters(mat = mat_FibroblastNucleiDiabetes, metadata = meta_FibroblastNucleiDiabetes$trt, if_log = TRUE)
 head(new_ref_matrix)
 tail(new_ref_matrix)
diff --git a/R/musMusculus/GSE124952/GSE124952.r b/R/musMusculus/GSE124952/GSE124952.r
index 546ceff..299da1a 100644
--- a/R/musMusculus/GSE124952/GSE124952.r
+++ b/R/musMusculus/GSE124952/GSE124952.r
@@ -34,7 +34,7 @@ checkRawCounts(as.matrix(mat_PFC))
 GSE124952Normalized <- NormalizeData(mat_PFC)
 GSE124952Normalized
 
-new_ref_matrix <- average_clusters(mat = mat_PFC, metadata = meta_PFC$CellType, if_log = TRUE)
+new_ref_matrix <- average_clusters(mat = GSE124952Normalized, metadata = meta_PFC$CellType, if_log = FALSE)
 new_ref_matrix_hashed <- average_clusters(mat = mat_PFC, metadata = meta_PFC$CellType, if_log = FALSE)
 head(new_ref_matrix)
 tail(new_ref_matrix)
diff --git a/R/musMusculus/GSE131957/GSE131957Beadneg1.R b/R/musMusculus/GSE131957/GSE131957Beadneg1.R
new file mode 100644
index 0000000..96bbe1c
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957Beadneg1.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832743_beadneg_dc1_1.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957Beadneg1.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957Beadneg2.R b/R/musMusculus/GSE131957/GSE131957Beadneg2.R
new file mode 100644
index 0000000..815395a
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957Beadneg2.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832744_beadneg_dc1_2.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957Beadneg1.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957TumorADT.R b/R/musMusculus/GSE131957/GSE131957TumorADT.R
new file mode 100644
index 0000000..8ad84ce
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957TumorADT.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832738_wt_tumor_adt.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957WTTumorADT.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957TumorGex.R b/R/musMusculus/GSE131957/GSE131957TumorGex.R
new file mode 100644
index 0000000..6c5ad1b
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957TumorGex.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832737_wt_tumor_gex.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957WTTumor.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957WTNaive.R b/R/musMusculus/GSE131957/GSE131957WTNaive.R
new file mode 100644
index 0000000..2b6cfe5
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957WTNaive.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832735_wt_naive_gex.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957WTNaiveADT.R b/R/musMusculus/GSE131957/GSE131957WTNaiveADT.R
new file mode 100644
index 0000000..d925cca
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957WTNaiveADT.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832736_wt_naive_adt.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957WTNaiveADT.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957ccr7k0Naive.R b/R/musMusculus/GSE131957/GSE131957ccr7k0Naive.R
new file mode 100644
index 0000000..1feb551
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957ccr7k0Naive.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832739_ccr7ko_naive_gex.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957ccr7koNaive.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957ccr7koADT.R b/R/musMusculus/GSE131957/GSE131957ccr7koADT.R
new file mode 100644
index 0000000..93bc623
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957ccr7koADT.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832740_ccr7ko_naive_adt.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957ccr7koNaiveADT.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957ccr7koTumor.R b/R/musMusculus/GSE131957/GSE131957ccr7koTumor.R
new file mode 100644
index 0000000..4e9460b
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957ccr7koTumor.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832741_ccr7ko_naive_gex.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957ccr7koNaive.rds")
diff --git a/R/musMusculus/GSE131957/GSE131957ccr7koTumorADT.R b/R/musMusculus/GSE131957/GSE131957ccr7koTumorADT.R
new file mode 100644
index 0000000..67cda75
--- /dev/null
+++ b/R/musMusculus/GSE131957/GSE131957ccr7koTumorADT.R
@@ -0,0 +1,41 @@
+library(dplyr)
+library(Seurat)
+library(patchwork)
+library(clustifyr)
+library(tidyverse)
+library(digest)
+library(here)
+
+proj_dir <- here()
+GSE131957 <- file.path(proj_dir, "Reference-Matrix-Generation", "data", "GSE131957_Raw 2", "GSM3832742_ccr7ko_tumor_adt.csv.gz")
+
+mat_mouseLungLesions <- read.csv(GSE131957)
+mat_mouseLungLesions <- mat_mouseLungLesions %>%
+  # as.data.frame() %>%
+  column_to_rownames('X')
+#  as.matrix() %>%
+#  t()
+mat_mouseLungLesions[1:5, 1:5]
+
+meta_mouseLungLesions <- read_csv("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE131nnn/GSE131957/suppl/GSE131957_single_cell_metadata.csv.gz")
+meta_mouseLungLesions <- meta_mouseLungLesions %>% column_to_rownames("X1") %>% t() %>% as.data.frame()
+meta2 <- meta_mouseLungLesions[colnames(mat_mouseLungLesions),]
+meta_mouseLungLesions
+sum(colnames(mat_mouseLungLesions) %in% meta_mouseLungLesions$cluster)
+ncol(mat_mouseLungLesions)
+
+source("~/Reference-Matrix-Generation/R/utils/utils.r")
+checkRawCounts(as.matrix(mat_mouseLungLesions))
+
+GSE131957WTNaiveNormalized <- NormalizeData(mat_mouseLungLesions)
+
+new_ref_matrix <- average_clusters(mat = GSE131957WTNaiveNormalized, metadata = meta2, cluster_col = "cluster_annotation", if_log = FALSE)
+new_ref_matrix_hashed <- average_clusters(mat = mat_mouseLungLesions, metadata = meta_mouseLungLesions, if_log = FALSE)
+head(new_ref_matrix)
+tail(new_ref_matrix)
+newcols <- sapply(colnames(new_ref_matrix_hashed), digest, algo = "sha1")
+colnames(new_ref_matrix_hashed) <- newcols
+head(new_ref_matrix_hashed)
+tail(new_ref_matrix_hashed)
+saveRDS(new_ref_matrix_hashed, "GSE131957Hashed.rds")
+saveRDS(new_ref_matrix, "GSE131957ccr7koTumorADT.rds")
diff --git a/R/musMusculus/mouseAtlas.r b/R/musMusculus/mouseAtlas.r
index 5716d4c..90e38bd 100644
--- a/R/musMusculus/mouseAtlas.r
+++ b/R/musMusculus/mouseAtlas.r
@@ -10,7 +10,7 @@ library(here)
 proj_dir <- here()
 
 # get scripts
-source(file.path(proj_dir, "R", "utils", "utils.r"))
+source(file.path(proj_dir, "Reference-Matrix-Generation", "R", "utils", "utils.r"))
 
 # path to matrices
 ref_matrix_dir <- file.path(proj_dir, "Reference-Matrix-Generation", "ref_matrices", "musMusculus")
diff --git a/atlas/musMusculus/MouseAtlas.rds b/atlas/musMusculus/MouseAtlas.rds
index 2059e3a..6c760c3 100644
Binary files a/atlas/musMusculus/MouseAtlas.rds and b/atlas/musMusculus/MouseAtlas.rds differ
diff --git a/data/GSE131957_RAW 2/GSM3832735_wt_naive_gex.csv.gz b/data/GSE131957_RAW 2/GSM3832735_wt_naive_gex.csv.gz
new file mode 100644
index 0000000..a648117
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diff --git a/data/GSE131957_RAW 2/GSM3832736_wt_naive_adt.csv.gz b/data/GSE131957_RAW 2/GSM3832736_wt_naive_adt.csv.gz
new file mode 100644
index 0000000..8eb18a4
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diff --git a/data/GSE131957_RAW 2/GSM3832737_wt_tumor_gex.csv.gz b/data/GSE131957_RAW 2/GSM3832737_wt_tumor_gex.csv.gz
new file mode 100644
index 0000000..76101d9
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diff --git a/data/GSE131957_RAW 2/GSM3832738_wt_tumor_adt.csv.gz b/data/GSE131957_RAW 2/GSM3832738_wt_tumor_adt.csv.gz
new file mode 100644
index 0000000..7118c78
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diff --git a/data/GSE131957_RAW 2/GSM3832739_ccr7ko_naive_gex.csv.gz b/data/GSE131957_RAW 2/GSM3832739_ccr7ko_naive_gex.csv.gz
new file mode 100644
index 0000000..490adda
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diff --git a/data/GSE131957_RAW 2/GSM3832740_ccr7ko_naive_adt.csv.gz b/data/GSE131957_RAW 2/GSM3832740_ccr7ko_naive_adt.csv.gz
new file mode 100644
index 0000000..4e8cdfc
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diff --git a/data/GSE131957_RAW 2/GSM3832741_ccr7ko_tumor_gex.csv.gz b/data/GSE131957_RAW 2/GSM3832741_ccr7ko_tumor_gex.csv.gz
new file mode 100644
index 0000000..d98152b
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diff --git a/data/GSE131957_RAW 2/GSM3832742_ccr7ko_tumor_adt.csv.gz b/data/GSE131957_RAW 2/GSM3832742_ccr7ko_tumor_adt.csv.gz
new file mode 100644
index 0000000..c6a60d1
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diff --git a/data/GSE131957_RAW 2/GSM3832743_beadneg_dc1_1.csv.gz b/data/GSE131957_RAW 2/GSM3832743_beadneg_dc1_1.csv.gz
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index 0000000..b416894
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diff --git a/data/GSE131957_RAW 2/GSM3832744_beadneg_dc1_2.csv.gz b/data/GSE131957_RAW 2/GSM3832744_beadneg_dc1_2.csv.gz
new file mode 100644
index 0000000..aa7988e
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diff --git a/data/GSE131957_RAW 2/GSM3832745_beadneg_dc1_3.csv.gz b/data/GSE131957_RAW 2/GSM3832745_beadneg_dc1_3.csv.gz
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index 0000000..b3f75a9
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diff --git a/data/GSE131957_RAW 2/GSM3832746_beadpos_dc1_1.csv.gz b/data/GSE131957_RAW 2/GSM3832746_beadpos_dc1_1.csv.gz
new file mode 100644
index 0000000..3412c95
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diff --git a/data/GSE131957_RAW 2/GSM3832747_beadpos_dc1_2.csv.gz b/data/GSE131957_RAW 2/GSM3832747_beadpos_dc1_2.csv.gz
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index 0000000..ba93fe0
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diff --git a/data/GSE131957_RAW 2/GSM3832748_beadpos_dc1_3.csv.gz b/data/GSE131957_RAW 2/GSM3832748_beadpos_dc1_3.csv.gz
new file mode 100644
index 0000000..eeb4ae2
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diff --git a/data/GSE131957_RAW 2/GSM3832749_gfpneg_dc1_1.csv.gz b/data/GSE131957_RAW 2/GSM3832749_gfpneg_dc1_1.csv.gz
new file mode 100644
index 0000000..4fc7918
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diff --git a/data/GSE131957_RAW 2/GSM3832750_gfpneg_dc1_2.csv.gz b/data/GSE131957_RAW 2/GSM3832750_gfpneg_dc1_2.csv.gz
new file mode 100644
index 0000000..a020a07
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diff --git a/data/GSE131957_RAW 2/GSM3832751_gfppos_dc1_1.csv.gz b/data/GSE131957_RAW 2/GSM3832751_gfppos_dc1_1.csv.gz
new file mode 100644
index 0000000..a564c07
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diff --git a/data/GSE131957_RAW 2/GSM3832752_gfppos_dc1_2.csv.gz b/data/GSE131957_RAW 2/GSM3832752_gfppos_dc1_2.csv.gz
new file mode 100644
index 0000000..c4ac59a
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diff --git a/data/GSE131957_RAW 2/GSM3832753_gfppos_dc1_3.csv.gz b/data/GSE131957_RAW 2/GSM3832753_gfppos_dc1_3.csv.gz
new file mode 100644
index 0000000..3b02944
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diff --git a/meta-analysis/Mouse-Meta-Analysis.r b/meta-analysis/Mouse-Meta-Analysis.r
index 6223f0b..434f37b 100644
--- a/meta-analysis/Mouse-Meta-Analysis.r
+++ b/meta-analysis/Mouse-Meta-Analysis.r
@@ -69,7 +69,7 @@ mouseMetaAnalysis.markers <- FindAllMarkers(mouseMetaAnalysis, only.pos = TRUE,
 mouseMetaAnalysis.markers %>% group_by(cluster) %>% top_n(n = 2, wt = avg_logFC)
 cluster1.markers <- FindMarkers(mouseMetaAnalysis, ident.1 = 0, logfc.threshold = 0.25, test.use = "roc", only.pos = TRUE)
 top10 <- mouseMetaAnalysis.markers %>% group_by(cluster) %>% top_n(n = 10, wt = avg_logFC) #Create top 10 markers for each cluster
-DoHeatmap(pbmc, features = top10$gene) + NoLegend() #Create heat map of top 10 markers
+DoHeatmap(mouseMetaAnalysis, features = top10$gene) + NoLegend() #Create heat map of top 10 markers
 
 #Assign cell types/Annotate UMAP
 new.cluster.ids <- colnames(mouseAtlas)
diff --git a/ref_matrices/musMusculus/GSE124952/GSE124952.rds b/ref_matrices/musMusculus/GSE124952/GSE124952.rds
index 4fec3cc..2ad6265 100644
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diff --git a/ref_matrices/musMusculus/GSE131957/GSE131957WTNaive.rds b/ref_matrices/musMusculus/GSE131957/GSE131957WTNaive.rds
new file mode 100644
index 0000000..c50ee33
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diff --git a/ref_matrices/musMusculus/GSE131957/GSE131957WTTumor.rds b/ref_matrices/musMusculus/GSE131957/GSE131957WTTumor.rds
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index 0000000..bb16c98
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diff --git a/ref_matrices/musMusculus/GSE131957/GSE131957ccr7koNaive.rds b/ref_matrices/musMusculus/GSE131957/GSE131957ccr7koNaive.rds
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diff --git a/ref_matrices/musMusculus/GSE131957/GSE131957ccr7koTumor.rds b/ref_matrices/musMusculus/GSE131957/GSE131957ccr7koTumor.rds
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