Publications by Kennedi Todd
Da Mesquita scRNAseq g:Profiler
Output below are interactive Manhattan plots. The x-axis has functional terms and the y-axis has the -log10(adjust p-value). The size of the circles corresponds to the term size. Term size is the number of genes in the pathway. So, GO:1234 (5) would have a smaller circle compared to GO:5678 (100) because there are 5 genes in GO:1234 pathway vs 10...
3555 sym
Da Mesquita scRNAseq Annotation
Setup Wet lab These were cell suspensions of meningeal dura, enriched by MACS for cells expressing Cd45, Cd31, and Lyve-1. We sent libraries from ~5000 cells per sample to be sequenced at least 50,000 reads per cell. We might have ended up with more though, because we sequenced in the NovaSeq S2. We are expecting to see a lot of leukocytes and v...
4426 sym R (65462 sym/170 pcs) 128 img
Da Mesquita: Recluster BECs and LECs
Setup Working directory knitr::opts_knit$set( root.dir = "/research/labs/neurology/fryer/m214960/Da_Mesquita/scripts/R") Libraries # load packages library(ComplexUpset) # intersection_size() library(dplyr) # ungroup() library(ggrepel) # geom_text_repel() library(gtools) # smartbind() library(harmony) # RunHarmony() libr...
1242 sym R (41328 sym/87 pcs) 48 img
Recluster T cells & ILCs
Setup Working directory knitr::opts_knit$set( root.dir = "/research/labs/neurology/fryer/m214960/Da_Mesquita/scripts/R") Libraries # load packages library(ComplexUpset) # intersection_size() library(dplyr) # ungroup() library(ggrepel) # geom_text_repel() library(gtools) # smartbind() library(harmony) # RunHarmony() libr...
1147 sym R (38831 sym/82 pcs) 42 img
Da Mesquita: Recluster myeloid cells
Setup Working directory knitr::opts_knit$set( root.dir = "/research/labs/neurology/fryer/m214960/Da_Mesquita/scripts/R") Libraries # load packages library(ComplexUpset) # intersection_size() library(dplyr) # ungroup() library(ggrepel) # geom_text_repel() library(gtools) # smartbind() library(harmony) # RunHarmony() libr...
1441 sym R (46420 sym/94 pcs) 53 img
Ola scRNAseq Processing Strict Thresholds
Background Tanner’s notes Based on findings in earlier paper, Clu knockout mice expressing APP saw a unique amyloid pathology where plaques moved from brain parenmycha (where they are usually found) to within blood vessels. Using a cell extraction method to enrich for vasculature and mural cells, we investigate using single cell RNA sequencin...
11491 sym R (48730 sym/142 pcs) 45 img
10x Genomics scRNAseq Integrated w/ Choroid Processing
Setup Set working directory knitr::opts_knit$set(root.dir = "/research/labs/neurology/fryer/m214960/10x_HIVE_PIPseq/10x/scripts/R/single_cell_with_choroid") Load libraries library(data.table) # fread() library(dplyr) # lef_join() ## ## Attaching package: 'dplyr' ## The following objects are masked from 'package:data.table': ## ## between,...
7985 sym R (39317 sym/137 pcs) 33 img
Gene Enrichment Analysis: Age and Isoform Up-regulated
Setup # load library library(gprofiler2) # read table isoform.df <- read.table("../../results/DEGs/E4_vs_E3_DEGs.tsv",sep="\t",header=TRUE) age.df <- read.table("../../results/DEGs/14_vs_2_months_DEGs.tsv",sep="\t",header=TRUE) sex.df <- read.table("../../results/DEGs/female_vs_male_DEGs.tsv",sep="\t",header=TRUE) # filter by pval isoform.df <-...
1254 sym R (638 sym/5 pcs)
Mouse scRNAseq Annotation
Setup Working directory knitr::opts_knit$set( root.dir = "/research/labs/neurology/fryer/m214960/Ferreira_Da_Mesquita/scripts/R") Libraries # load packages library(ComplexUpset) # upset() library(dplyr) library(ggrepel) # geom_text_repel() library(ggtree) # BuildClusterTree() library(gtools) library(gridExtra) library(parallel) # detectCores(...
3984 sym R (56768 sym/200 pcs) 65 img
All Cluster Annotations
Setup Working directory knitr::opts_knit$set( root.dir = "/research/labs/neurology/fryer/m214960/Ferreira_Da_Mesquita/scripts/R") Libraries # load packages library(ComplexUpset) # upset() library(dplyr) library(ggrepel) # geom_text_repel() library(ggtree) # BuildClusterTree() library(gtools) library(gridExtra) library(parallel) # detectCores(...
3998 sym R (59124 sym/205 pcs) 66 img