Publications by Nadine Bestard
Document
Setup # libraries library(Seurat) # for scrnaseq analyisis ## Attaching SeuratObject library(here) # for reproducible paths ## here() starts at C:/Users/nbestard/OneDrive/Luise_HCA library(ggplot2)# for adding some custom to the seurat plots library(patchwork) # for adding customs to grid-composed Seurat plots library(ggsci) # colors # Set ...
2367 sym R (9936 sym/47 pcs) 11 img
HCA all celltypes INDEX
HCA This is just a complementary repository where I (Nadine Bestard) will work on bits and pieces of the HCA project from Luise Seeker. First objective: Integration/Merging tissue datasets, clustering and celltype identification and annotation Source (Src) and Documents (Docs) The analysis is summarised in main.R, a script that calls in the corr...
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Compare rodents with HCA
Libraries Load objects Are the genes de in rodents expressed in the HCA dataset This first chunck of code aims to check if the genes already highlited as potential “old” markers from the rodents data are present in the human dataset from the HCA ## [1] 49 ## [1] "Ube2c" "Gp1bb" 49 genes are present, Ube2c, Gp1bb are the two absent. Young a...
1335 sym R (6495 sym/9 pcs) 4 img
Integrate adults with embryos
Setup # libraries library(Seurat) # for scrnaseq analyisis ## Attaching SeuratObject library(here) # for reproducible paths ## here() starts at C:/Users/nbestard/OneDrive/Laura Load objects srt_old <- readRDS(here("Data", "HCA", "srt_opcs.RDS")) srt_dev <- readRDS(here("Data", "Embryos", "hca_dev_scanpy_harmony_opcs.rds")) The seurat adult o...
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Rat differential expression
Obtain data The data has been downloaded from GEO at the accession GSE134765. This provides the features counts output that have been transformed into a counts matrix with doRawMatrix.sh script, available in AW gitHub. The column names have been simplified with: # Remove the ".//" from the beggining of the column names. sed -i -e "1s/\.\/\///g" ...
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Compare published young-old DE from rat and mouse
Summary I have compared the genes highlighted as deferentially expressed between old and young OPCs from published rat and mouse DE analysis. The rat data-set has been obtain from “Metformin Restores CNS Remyelination Capacity by Rejuvenating Aged Stem Cells”, Neumann et al. In the supplementary data they provide the young-old DE analysis fo...
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Compare young-old DE from rat and mouse
Obtain data Comparing genes differentially expressed between young and old mice and rat. The raw data from rat bulk RNAseq has been downloaded from GEO at the accession GSE134765 (Neumann et al. 2019). The differential expression analysis between young and old rat was done following DESeq2 workflow (Love, Huber, and Anders 2014) The mouse differe...
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README - Compare young-old DE from rat and mouse
Do adult human oligodendrocytes remyelinate poorly and can we change this to better treat progressive multiple sclerosis? Aim This project covers the first aim of the project: 1) Determine whether adult human oligodendroglia in adult brain tissue in health and in MS express markers of ageing similar to those in aged rat Contains Compare species...
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Cluster QC
Set up # libraries library(Seurat) # for scrnaseq analyisis ## Attaching SeuratObject library(here) # for reproducible paths ## here() starts at C:/Users/nbestard/OneDrive/Luise_HCA library(ggplot2) # plots library(ggsci) # colors # Set up the color palette mypal <- pal_npg("nrc", alpha = 0.7)(10) mypal2 <-pal_tron("legacy", alpha = 0.7)(7) ...
2287 sym R (5388 sym/27 pcs) 7 img
Cluster QC 2
Set up # libraries library(Seurat) # for scrnaseq analyisis ## Attaching SeuratObject library(here) # for reproducible paths ## here() starts at C:/Users/nbestard/OneDrive/Luise_HCA library(ggplot2) # plots library(ggsci) # colors # Set up the color palette mypal <- pal_npg("nrc", alpha = 0.7)(10) mypal2 <-pal_tron("legacy", alpha = 0.7)(7) ...
1571 sym R (4895 sym/25 pcs) 5 img