Publications by Nadine Bestard
Cell and gene QC (young-jpriller)
Set-up The object has 32285 genes and 90750 cells before filtering Add cell QC metrics to the sce First we need to sort the gene names and gene symbols, because the default ensembl notation is not very handy. And then save the mitochondrial genes as such. Then we can use the scater package to add the quality per cell. This computes for each cell...
4057 sym R (3933 sym/5 pcs) 16 img
Batch correction (young-jpriller)
Set-up library(here) # for reproducible paths library(SingleCellExperiment) library(scater) # For qc and visualisation library(scran) # For normalisation library(Matrix) # For log transorming the raw data library(ggplot2) # To add titles to plots library(batchelor) # Batch correction # Adapted function from VISION to log tranform sparse mat...
1656 sym R (6858 sym/13 pcs) 3 img
First QC (VM)
Set-up The object has 32285 genes and 63430 cells before filtering Add cell QC metrics to the sce First we need to sort the gene names and gene symbols, because the default ensembl notation is not very handy. And then save the mitochondrial genes as such. Then we can use the scater package to add the quality per cell. This computes for each cell...
4057 sym R (4062 sym/5 pcs) 16 img
Batch correction (VM)
Set-up library(here) # for reproducible paths library(SingleCellExperiment) library(scater) # For qc and visualisation library(scran) # For normalisation library(Matrix) # For log transorming the raw data library(ggplot2) # To add titles to plots library(batchelor) # Batch correction # Adapted function from VISION to log tranform sparse mat...
1658 sym R (6864 sym/13 pcs) 3 img
Subsetting oligos
Set-up library(here) # for reproducible paths library(SingleCellExperiment) library(scater) # For qcs library(dplyr) # df manipulation library(scran) # For feature selcetion library(ggplot2) # To add titles to plots library(batchelor) # Batch correction Import We import the dataset and subset for the clusters that had highest expression of...
2373 sym R (6883 sym/39 pcs) 23 img
Clustering oligos (VM)
Set-up The workflow and explanations bellow are from OSCA Motivation Clustering is an unsupervised learning procedure that is used in scRNA-seq data analysis to empirically define groups of cells with similar expression profiles. It is worth stressing the distinction between clusters and cell types. The former is an empirical construct while the...
1300 sym R (720 sym/5 pcs) 6 img
annotation (VM)
Clustering at k60 ## Scale for 'colour' is already present. Adding another scale for 'colour', ## which will replace the existing scale. Annotation We make a first rough annotation using known markers for different celltypes. Click to expand the Neurons marker plots ## Scale for 'colour' is already present. Adding another scale for 'colour',...
856 sym R (1785 sym/15 pcs) 31 img
Differential expression WTvsKO - edgeR (VM)
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, ...
759 sym R (5267 sym/46 pcs) 2 img
Clustering 01 young (jpriller)
Set-up The workflow and explanations bellow are from OSCA library(SingleCellExperiment) library(here) #reproducible paths library(scater) # Plot dimred library(bluster) # Clustering library(clustree) # show relationship clustering #library(Seurat) # clusternig 2 library(pals) # for palettes with large n #kelly()22, #polychrome()#36, unname...
1416 sym R (6800 sym/28 pcs) 22 img
From QC to batch correct 2- young (jpriller)
Set-up library(here) # for reproducible paths library(SingleCellExperiment) library(scater) # For qcs library(scran) # for normalisation, feature selection library(ggplot2) # To add titles to plots library(batchelor) # Batch correction library(patchwork) # agregate plots library(pals) # for palettes with large n project <- "fire-mice" sce...
973 sym R (6795 sym/37 pcs) 17 img