Publications by Nadine Bestard
first.step(worklowr)
testworkflowR Home About License workflowr Summary Checks Past versions Last updated: 2022-01-21 Checks: 7 0 Knit directory: testworkflowR/ This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The...
3516 sym R (1730 sym/5 pcs) 1 img 1 tbl
microglia DE jpriller young
set-up library(SingleCellExperiment) # manipulate sce library(scater) # plots library(here) # reproducible paths library(miloR) # DA abundance package library(dplyr) # distinct library(patchwork) #plots Milo vignette followed for this analyisis: miloR source(here("src/colours.R")) project <- "fire-mice" sce <- readRDS(here("processed", pro...
6299 sym R (9412 sym/36 pcs) 6 img
DA barplots young (jpriller)
set-up library(SingleCellExperiment) library(here) # reproducible paths library(scater) # plot reduced dims library(dplyr) #manipulate df library(pals) # for palettes with large n #kelly()22, #polychrome()#36, cols25() project <- "fire-mice" sce <- readRDS(here("processed", project,"sce_nodbl_anno_02.RDS")) source(here("src/colours.R")) Dime...
264 sym R (3068 sym/9 pcs) 3 img
Annotation 02 young (jpriller)
R Analysis for fire mice scRNAseq OLD Done: The first cell and gene quality control is in QC The normalisation by deconvolution is in normalise Feature selection and dimensional reduction in feature_selection_dimred Clustering at different resolutions, clustering_01 First rough annotation in annotation_01 Cluster QC in clusterQC_k5, now includes...
2042 sym
Annotation 02 young (0.2) (jpriller)
library(here) #reproducible paths library(scater) #feature plots library(patchwork) # agregate plots library(scran) # for findmarkers library(pals) # for palettes with large n #kelly()22, #polychrome()#36, cols library(tidyverse) # edit project <- "fire-mice" cols25 <- unname(cols25()) # remove the black and white from the pallete, and the...
2068 sym R (21411 sym/60 pcs) 34 img
Clustering 02 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...
1626 sym R (9457 sym/31 pcs) 22 img
Differential expression WTKOand WTHET - edgeR (jpriller)
set-up library(scran) # for scDE ## Warning: package 'scran' was built under R version 4.1.2 ## Loading required package: SingleCellExperiment ## Loading required package: SummarizedExperiment ## Loading required package: MatrixGenerics ## Loading required package: matrixStats ## ## Attaching package: 'MatrixGenerics' ## The following objects a...
2872 sym R (8009 sym/54 pcs)
BAMs Hetvsko
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", project, "sce_anno_02.RDS")) dir.create(here("outs", project, "DE_edgeR"), showWarnings = FALSE, recursive = TRUE) dir.create(here("processed", project), sh...
351 sym R (2329 sym/12 pcs) 4 img
clusterQC young (jpriller)
set-up library(SingleCellExperiment) library(here) # reproducible paths library(scater) # plot reduced dims library(tibble) # for `rownames_to_column` library(scDblFinder) # detect doublets library(pals) # for palettes with large n #kelly()22, #polychrome()#36, unname(alphabet()) library(dplyr) # df filtering project <- "fire-mice" if (!fi...
4725 sym R (13324 sym/35 pcs) 9 img
index jpriller
R Analysis for fire mice scRNAseq Overall cellrangerQC OLD Done: The first cell and gene quality control is in QC The normalisation by deconvolution is in normalise Feature selection and dimensional reduction in feature_selection_dimred Clustering at different resolutions, clustering_01 First rough annotation in annotation_01 Cluster QC in clust...
2078 sym