Publications by Ehsan Razmara Monash Uni
venn graph
library(ggplot2) library(ggvenn) ## Loading required package: 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 ## Loading required package: grid library(ggVennDiagram) gene...
22 sym R (840 sym/13 pcs) 4 img
radar_plot
scores <- data.frame( row.names = c("Naive CD4 T", "CD14+ Mono" , "Memory CD4 T"), LDHB = c(7.9, 3.9, 9.4), S100A9 = c(10, 20, 0), IL32 = c(3.7, 11.5, 2.5), CD79A = c(8.7, 20, 4), CCL5 = c(7.9, 7.2, 12.4), MS4A7 = c(6.4, 10.5, 6.5), GZMB = c(2.4, 0.2, 9.8), FCER1A = c(0, 0, 20), PF4 =...
19 sym R (2352 sym/11 pcs) 3 img
raceid
library(RaceID) library(Seurat) ## Attaching SeuratObject 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) pbmc <- readRDS("/mnt/nectar_volume/hom...
2688 sym R (49104 sym/55 pcs) 26 img
volcano_seurat
library(Seurat) ## Attaching SeuratObject library(SeuratWrappers) library(ggplot2) 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 pbmc_tutorial_final <- readRDS(...
120 sym R (5260 sym/14 pcs) 1 img
heatmap enhancement
library(RColorBrewer) library(Seurat) ## Attaching SeuratObject 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(RColorBrewer) library(pheatmap) library(Co...
42 sym R (6435 sym/33 pcs) 4 img
cell cycle regression
As the "cc.genes$s.genes/g2m.genes have been written for Human, we are supposed to change the organism here, i.e., we need to align all genes in mice. To this end, we should use the following functions. library(biomaRt) library(Seurat) ## Attaching SeuratObject library(org.Hs.eg.db) ## Loading required package: AnnotationDbi ## Loading required p...
637 sym R (23125 sym/58 pcs) 6 img
Liger
library(rliger) ## Loading required package: cowplot ## Loading required package: Matrix ## Loading required package: patchwork ## ## Attaching package: 'patchwork' ## The following object is masked from 'package:cowplot': ## ## align_plots library(Seurat) ## Attaching SeuratObject library(SeuratData) ## ── Installed datasets ───�...
152 sym R (14545 sym/51 pcs) 1 img
Seurat obj batch effect elimination
library(Seurat) ## Attaching SeuratObject library(SeuratData) ## ── Installed datasets ───────────────────────────────────── SeuratData v0.2.2 ── ## ✓ ifnb 3.1.0 ✓ pbmcsca 3.0.0 ## ✓ panc8 3.0.2 ## ───────────...
292 sym R (4244 sym/31 pcs) 1 img
harmony batch effect elimination
Herein, we will utilise the Signac R package’s Harmony batch effect correction method (Korsunsky et al. 2019). The Harmony algorithm is accessible on GitHub, and Signac provides integration tutorials. library(dplyr) ## ## Attaching package: 'dplyr' ## The following objects are masked from 'package:stats': ## ## filter, lag ## The followi...
886 sym R (5671 sym/66 pcs) 2 img
seurat stacked vlnplot
library(Seurat) ## Attaching SeuratObject library(SeuratWrappers) library(ggplot2) 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 pbmc_tutorial_final <- readRDS(...
120 sym R (5260 sym/14 pcs) 1 img