InstallData("pbmc3k") error

[partrita]

Using cached data manifest, last updated at 2023-06-16 14:55:40

Error: No access to remote SeuratData repository, unable to install new datasets
Traceback:

1. InstallData("pbmc3k")
2. stop("No access to remote SeuratData repository, unable to install new datasets", 
 .     call. = FALSE)

I guess, This repo not maintained properly.

[andreagrioni]

I have the same issue, I tried the solution here but it did not sove it.

[crystalizee]

exact same error

[KSDalton]

exact same error, and the same error happens to other SeuratData sets, including panc8 and pbmcsca

[bbimber]

We're also hitting this issue. Did anyone find a solution?

[afrias90]

I had this issue for the 'ifnb' dataset (but i can grab the pbmc3k dataset too now), I was able to solve this with downloading devtools (may require restarting R) Install devtools from CRAN install.packages("devtools")

Or the development version from GitHub: install.packages("devtools") devtools::install_github("r-lib/devtools")

and also using the link provided in another answer: install.packages("https://seurat.nygenome.org/src/contrib/ifnb.SeuratData_3.0.0.tar.gz", repos = NULL, type = "source")

Don't forget load the library library(SeuratData) InstallData("pbmc3k")

Otherwise, I originally got the raw data from here, unzipped with with untar() and manually put the file 'filtered_gene_bc_matrices' in my workspace to overcome that first step. Edit: untar() or some process requires library(devtools) as I kept getting an error without it as I'm doing something else https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz

[ahdee]

This issue seem to come up a lot; here is my solution for panc8 but is the same regardless of what dataset you are trying to download.

# note the version of seurat, else use UpdateSeuratObject
AvailableData()

## I suspect that failing is due to network error timing out. 
# failed -- however copy the url 
InstallData("panc8")

# failed 
install.packages("https://seurat.nygenome.org/src/contrib/panc8.SeuratData_3.0.2.tar.gz", repos = NULL, type = "source")

## go to bash and use <cd /tmp; wget https://seurat.nygenome.org/src/contrib/panc8.SeuratData_3.0.2.tar.gz>
install.packages("/tmp/panc8.SeuratData_3.0.2.tar.gz", repos = NULL, type = "source")

# then load it, do not just load panc8 
library (panc8.SeuratData )
data("panc8")
# my is ver 4  so  I need to update the data 
panc8<-UpdateSeuratObject(panc8)
## works as expected now! 

pancreas.list <- SplitObject(panc8, split.by = "tech")
pancreas.list <- pancreas.list[c("celseq", "celseq2", "fluidigmc1", "smartseq2")]

[IrinaVKuznetsova]

same here pbmc3k <- LoadData("pbmc3k") "Error: Cannot find dataset pbmc3k"

[partrita]

same here pbmc3k <- LoadData("pbmc3k") "Error: Cannot find dataset pbmc3k"

for pbmc3k data set, just download this

Try this.

library(Seurat)
pbmc.data <- Read10X(data.dir = "../data/pbmc3k/filtered_gene_bc_matrices/hg19/")
pbmc <- CreateSeuratObject(counts = pbmc.data, project = "pbmc3k", min.cells = 3, min.features = 200)
pbmc

[AzureLii]

same erro, Seems to be a network problem, you can try to download several times, and try to keep on the Rstudio download bar page.....

[partrita]

same erro, Seems to be a network problem, you can try to download several times, and try to keep on the Rstudio download bar page.....

You could manually download files and make a seurat object.

[AzureLii]

same erro, Seems to be a network problem, you can try to download several times, and try to keep on the Rstudio download bar page.....

You could manually download files and make a seurat object.

Thanks！This is also a good idea, tody, I found another method - installing packages locally. For details, please refer to: https://github.com/satijalab/seurat-data/issues/15