analyzing a single cell and searching for a specific gene using single cell data

Question

[Bioinfo]

Hi guys,

I am trying to find the expression of a given gene across various organism in this dataset

https://figshare.com/articles/dataset/tms_gene_data_rv1/12827615

I can create my data using R from droplet

counts <- readMM("matrix.mtx")
genes <- read_tsv("genes.tsv", col_names = FALSE)
gene_ids <- genes$X1
cell_ids <- read_tsv("barcodes.tsv", col_names = FALSE)$X1
rownames(counts) <- gene_ids
colnames(counts) <- cell_ids

Now I want to know how to see the expression of Sirt1 in various cell lines. Does anyone know how to do it?

[rpolicastro]

They provide an h5ad file, which may contain the already processed data, plus associated cell and feature metadata. If so, you should load the h5ad as AnnData (Python), a SingleCellExperiment (R), or a Seurat object (R). Read the associated documentation for each package for exploration and plotting of data.

[Bioinfo]

rpolicastro yes they do have the h5ad data but I cannot figure how to make a use out of it. It seems they just cluster things and that is all about it. My biggest question how to get or follow only one gene , do you have any idea?

[jared.andrews07]

rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer also explain how to manipulate this data. Please explore the resources provided, they have all of the information you need.

Answer 1

[jared.andrews07]

I'd recommend you read what goes into a single cell analysis. The Orchestrating Single Cell Analysis or Seurat vignettes are a good place to start.

Depending on how you want to show the data, you may want a feature plot or maybe a box/violin plot.