Publications by Kennedi Todd
Document
Libraries library(dplyr) ## ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ## ## filter, lag ## The following objects are masked from 'package:base': ## ## intersect, setdiff, setequal, union library(ggplot2) library(plotly) ## ## Attaching package: 'plotly' ## The following object is masked from...
271 sym R (5463 sym/13 pcs)
Publish Document
Setup Working directory knitr::opts_knit$set(root.dir = ".") Libraries library(plotly) # plot_ly() library(tidyr) # pivot_longer() User defined variables out <- "../../results/all_samples_strict/" out2 <- "all_samples_strict" model <- "DEGs_both_sexes/" treatment_order <- c("saline","psilocybin") treatment_colors <- c("gray60","springgreen2") s...
186 sym R (11288 sym/8 pcs)
Psilo1 Figures
Setup Working directory knitr::opts_knit$set(root.dir = ".") Libraries library(plotly) # plot_ly() library(tidyr) # pivot_longer() User defined variables out <- "../../results/all_samples_strict/" out2 <- "all_samples_strict" model <- "DEGs_both_sexes/" treatment_order <- c("saline","psilocybin") treatment_colors <- c("gray60","springgreen2") s...
158 sym R (3499 sym/6 pcs)
Meningitis Meninge Gprofiler2
Background g:GOSt performs functional enrichment analysis on an input gene list. It maps genes to known functional information sources and detects statistically significantly enriched terms. Data is regularly retrieved from Ensembl database and fungi, plants or metazoa specific versions of Ensembl Genomes, and parasite specific data from WormBase...
925 sym R (647 sym/4 pcs)
Functional Enrichment Analysis
Background g:GOSt performs functional enrichment analysis on an input gene list. It maps genes to known functional information sources and detects statistically significantly enriched terms. Data is regularly retrieved from Ensembl database and fungi, plants or metazoa specific versions of Ensembl Genomes, and parasite specific data from WormBase...
925 sym R (677 sym/4 pcs)
All Clusters Pass 1 Annotation
Setup Experiment notes 16 scRNAseq samples of meningeal endothelial cells were sent for sequencing. In this experiment we treated E3 and E4, male and female mice (12-month-old), with a control diet or a PLX5622 diet (to ablate MHC-II high myeloid cells in the meninges), and we intend to see the effects on the transcriptome of BECs and LECs. This w...
2638 sym R (27604 sym/102 pcs) 71 img
Meningeal Dura scRNAseq: Pass 1 All Clusters
Setup Notes Cell suspensions of meningeal dura enriched by MACS for cells expressing Cd45, Cd31, and Lyve-1 Cd45/Ptprc/B220/Ly-5/Lyt-4/T200: transmembrane protein tyrosine phosphatase, located on most haematopoietic cells, positive selection of leukocytes Cd31/Pecam1: adhesion and signaling receptor that is expressed on endothelial and hematopo...
3751 sym R (26202 sym/103 pcs) 75 img
Aducanumab Study: Adu.M.705A
Setup Set working directory knitr::opts_knit$set(root.dir = "/research/labs/neurology/fryer/m214960/aducanumab/scripts/R") Load libraries # load libraries library(cowplot) # plot_grid() library(dplyr) # left_join() library(ggplot2) # ggplot() library(gridExtra) # grid.arrange() library(harmony) # RunHarmony() library(parallel) ...
1728 sym R (29459 sym/84 pcs) 48 img
Aducanumab Study: IgG.M.851A
Setup Set working directory knitr::opts_knit$set(root.dir = "/research/labs/neurology/fryer/m214960/aducanumab/scripts/R") Load libraries # load libraries library(cowplot) # plot_grid() library(dplyr) # left_join() library(ggplot2) # ggplot() library(gridExtra) # grid.arrange() library(harmony) # RunHarmony() library(parallel) ...
1682 sym R (28397 sym/76 pcs) 40 img
Aducanumab Study: Adu.F.738B
Setup Set working directory knitr::opts_knit$set(root.dir = "/research/labs/neurology/fryer/m214960/aducanumab/scripts/R") Load libraries # load libraries library(cowplot) # plot_grid() library(dplyr) # left_join() library(ggplot2) # ggplot() library(gridExtra) # grid.arrange() library(harmony) # RunHarmony() library(parallel) ...
1682 sym R (28291 sym/76 pcs) 40 img