Publications by Ehsan Razmara Monash Uni
NichenetR, Kelly et al. E11.5, hindlimb
library(nichenetr) ## Registered S3 method overwritten by 'spatstat.geom': ## method from ## print.boxx cli library(Seurat) ## Attaching SeuratObject library(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── #...
105 sym R (11507 sym/41 pcs) 6 img
Monocle 3 performed on Kelly et al. E11.5 data
library(monocle3) ## Loading required package: Biobase ## Loading required package: BiocGenerics ## Loading required package: parallel ## ## Attaching package: 'BiocGenerics' ## The following objects are masked from 'package:parallel': ## ## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, ## clusterExport, clusterMap, parApply,...
1277 sym R (1002835 sym/62 pcs) 6 img
E11.5 Kelly et al. Hindlimb data (Seurat analysis)
pbmc.data <- Read10X(data.dir = "/mnt/nectar_volume/home/eraz0001/KELLY 2020/E11.5/") The most important stage is preparing Seurat object. pbmc.data[c("Lyz1", "Hoxd13", "Cdh5"), 1:30] ## 3 x 30 sparse Matrix of class "dgCMatrix" ## [[ suppressing 30 column names 'AAACCTGAGACGCACA-1', 'AAACCTGCACAGACAG-1', 'AAACCTGCAGGCTCAC-1' ... ]] ## ...
1096 sym R (15910 sym/133 pcs) 38 img
clustered dotplot for single-cell RNAseq E11.5 GSE142425
library(Seurat) ## Registered S3 method overwritten by 'spatstat.geom': ## method from ## print.boxx cli ## Attaching SeuratObject library(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ## ✓ ggplot2 3.3.5...
63 sym R (11506 sym/55 pcs) 3 img
Reactome E11.5 Kelly et al. GSE142425 Hindlimb 2
library(Seurat) ## Registered S3 method overwritten by 'spatstat.geom': ## method from ## print.boxx cli ## Attaching SeuratObject library(reactome.db) ## Loading required package: AnnotationDbi ## Loading required package: stats4 ## Loading required package: BiocGenerics ## Loading required package: parallel ## ## Attaching package: 'Bi...
61 sym R (11300 sym/51 pcs) 16 img
GO annotation on Kelly et al data E11.5 hindlimb dev
library(patchwork) library(enrichplot) ## library("clusterProfiler") ## clusterProfiler v3.18.1 For help: https://guangchuangyu.github.io/software/clusterProfiler ## ## If you use clusterProfiler in published research, please cite: ## Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological th...
296 sym R (21305 sym/105 pcs) 3 img
Cellchat E11.g Kelly et al. hindlimb mouse
library(CellChat) ## 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: igraph ## ## Attaching package: 'igraph' ## Th...
833 sym R (32394 sym/93 pcs) 51 img
E11.5 Kelly et al. Hindlimb data (SingleR)
SingleR annotation library(SingleR) ## Loading required package: SummarizedExperiment ## Loading required package: MatrixGenerics ## Loading required package: matrixStats ## ## Attaching package: 'MatrixGenerics' ## The following objects are masked from 'package:matrixStats': ## ## colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,...
76 sym R (18112 sym/49 pcs) 1 img
GSEA Kelly 2020 Hindlimb
library(Seurat) ## Registered S3 method overwritten by 'spatstat.geom': ## method from ## print.boxx cli ## Attaching SeuratObject library(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ## ✓ ggplot2 3.3.5...
56 sym R (53602 sym/49 pcs) 2 img
stackedvlnplot_seurat_two_groups
library(Seurat) ## Attaching SeuratObject library(SeuratData) ## ── Installed datasets ───────────────────────────────────── SeuratData v0.2.2 ── ## ✓ ifnb 3.1.0 ✓ pbmcsca 3.0.0 ## ✓ panc8 3.0.2 ## ───────────...
274 sym R (11431 sym/23 pcs) 1 img