Publications by Nadine Bestard
annotation 01 young (jpriller)
library(scater) #feature plots # the devel version for repel. library(here) # reproducible paths library(patchwork) # agregate plots library(scran) # for findmarkers library(pals) # for palettes with large n #kelly()22, #polychrome()#36, unname(alphabet()) project <- "fire-mice" cols25 <- unname(cols25()) # remove the black and white from th...
754 sym R (18445 sym/58 pcs) 34 img
miloR oligo old (jpriller)
Package library(miloR) # compositional analysis library(here) # reproducible paths library(scater) # sc plots library(dplyr) # modify design df library(ggplot2) #plots This analysis have been done following the MiloR vignette Load data For this study we will load our processed single cell experiment with subsetted oligos project <- "old" sc...
7906 sym R (13334 sym/56 pcs) 11 img
Normalisation 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 # Adapted function from VISION to log tranform sparse matrix # I could not download the package...
2873 sym R (7295 sym/15 pcs) 7 img
Workshop RNAseq
Libraries library(airway) # for my data library(Rsamtools) # to import the BAM files library(GenomicFeatures) # to import GTF file library(GenomicAlignments) # for summarizeoverlaps, counting reads library(DESeq2) # DE analysis library(pheatmap) # plot heatmap sample distances library(RColorBrewer) # create nice color plaettes library(ggpl...
711 sym R (7182 sym/45 pcs) 6 img
DA miloR old (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...
7942 sym R (10492 sym/43 pcs) 8 img
Subsetting oligos (jpriller)
Set-up Import Cell and gene QC We need to bear in mind this dataset comes from a bigger dataset where outliers have already been excluded. Violin plots ## Scale for 'colour' is already present. Adding another scale for 'colour', ## which will replace the existing scale. ## Scale for 'colour' is already present. Adding another scale for 'col...
1561 sym R (1363 sym/17 pcs) 27 img
Differential abundance of cells between KO-WT oligo clusters (VM)
set-up Dimensional reduction ## Scale for 'colour' is already present. Adding another scale for 'colour', ## which will replace the existing scale. ## Scale for 'colour' is already present. Adding another scale for 'colour', ## which will replace the existing scale. ## Warning: Removed 2 rows containing missing values (geom_text). ## Warnin...
1330 sym R (680 sym/4 pcs) 2 img
Differential expression WTvsKO - per cluster (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, ...
2419 sym R (6718 sym/48 pcs)
Normalisation by deconvolution (VM)
Set-up Normalisation by deconvolution In order to correct for systematic differences in sequencing coverage between libraries we will normalise the dataset. This involves dividing all counts for each cell by a cell-specific scaling factor, often called a “size factor” (Anders and Huber 2010). The assumption here is that any cell-specific bia...
2861 sym R (3923 sym/5 pcs) 7 img
Veronique miron index
Veronique Miron: Fire mice Done Only import the WT and KO (not the HET) The first cell and gene quality control Normalisation by deconvolution Feature selection and dimensional reduction Batch correction Clustering at different resolutions First rough annotation Subset the Oligodendrocytes: Stricter cell and gene QC feature selection batch co...
859 sym