Publications by Nadine Bestard
DE WTKO clusters vold jpriller
set-up library(scran) # for scDE library(scater) # for aggregate counts library(edgeR) #for De library(here) # reproducible paths library(DropletUtils) # ambient RNA library(scuttle) # modify gene names source(here("src/colours.R")) project <- "fire-mice" sce <- readRDS(here("processed", project, "sce_anno_02.RDS")) Use of pseudo-bulk sam...
3260 sym R (12718 sym/13 pcs)
vold DE oligo
set-up library(scran) # for scDE ## Loading required package: SingleCellExperiment ## Loading required package: SummarizedExperiment ## Loading required package: MatrixGenerics ## Loading required package: matrixStats ## ## Attaching package: 'MatrixGenerics' ## The following objects are masked from 'package:matrixStats': ## ## colAlls, ...
920 sym R (6234 sym/52 pcs) 9 img
de opc1vs2 jpriller vold
set-up library(scran) # for scDE ## Loading required package: SingleCellExperiment ## Loading required package: SummarizedExperiment ## Loading required package: MatrixGenerics ## Loading required package: matrixStats ## ## Attaching package: 'MatrixGenerics' ## The following objects are masked from 'package:matrixStats': ## ## colAlls, ...
953 sym R (6217 sym/52 pcs) 10 img
colour palette
library(pals) # for palettes with large n #kelly()22, #polychrome()#36, cols I will create a very big palette merging different colour palettes from pals. Kelly pal.bands(kelly()) From this palette I will remove black and white, as well as the light blue, similar to the cols25 one. # remove the black and white from the pallete, and the light ...
834 sym R (789 sym/8 pcs) 7 img
DE_oligo3_vold_jpriller
set-up library(scran) # for scDE library(scater) # for aggregate counts library(edgeR) #for De library(here) # reproducible paths project <- "fire-mice" sce <- readRDS(here("processed", "fire-mice", "sce_anno_02.RDS")) Oligo 1 vs Oligo 3 sce <- sce[,sce$clusters_named %in% c("mOligo1", "mOligo3")] sce$clusters_named <- droplevels(sce$clust...
850 sym R (4278 sym/22 pcs) 12 img
pseudotimeoligos
Set-up library(here) # paths ## here() starts at U:/Datastore/CMVM/scs/groups/jpriller-GROUP/scRNAseq/R-analysis-young library(scran) # feature select ## Loading required package: SingleCellExperiment ## Loading required package: SummarizedExperiment ## Loading required package: MatrixGenerics ## Loading required package: matrixStats ## ## Atta...
2981 sym R (23337 sym/109 pcs) 29 img
QC_02vold
Set-up library(here) # for reproducible paths library(SingleCellExperiment) library(scater) # For qcs library(ggplot2) # To add titles to plots library(patchwork) # agregate plots project <- "fire-mice" sce <- readRDS(here("processed", project, "sce_clusterQC.RDS")) source(here("src/colours.R")) The object has 23012 genes and 18481 cells. ...
907 sym R (5662 sym/32 pcs) 11 img 1 tbl
annotation_02_vold_jpriller
Set-up library(here) #reproducible paths library(scran) #aggregate library(scater) # plot sc library(scran) # for findmarkers library(readxl) # read the anotation file project<- "fire-mice" source(here("src/colours.R")) Loading sce <- readRDS(here("processed", project, "sce_clusters_02.RDS")) previous annotaion plotTSNE(sce, colour_by= "cl...
327 sym R (4617 sym/29 pcs) 13 img
clustering 02 vold
Set-up The workflow and explanations bellow are from OSCA library(SingleCellExperiment) library(here) #reproducible paths library(scater) # Plot dimred library(clustree) # show relationship clustering library(Seurat) # clusternig project<- "fire-mice" source(here("src/colours.R")) if(!file.exists(here("processed", project, "sce_clusters_02....
1089 sym R (4034 sym/19 pcs) 14 img
DA_miloR_vold_jpriller
Package library(miloR) # compositional analysis library(here) # reproducible paths library(scater) # sc plots library(dplyr) # modify design df This analysis have been done following the (MiloR vignette)[https://rawcdn.githack.com/MarioniLab/miloR/7c7f906b94a73e62e36e095ddb3e3567b414144e/vignettes/milo_gastrulation.html#5_Finding_markers_of_DA...
7890 sym R (11484 sym/45 pcs) 7 img