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welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets
GNU General Public License v3.0
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Called from: CheckPackage(package = "MacoskoLab/liger", repository = "github") #209

Closed edbels closed 3 years ago

edbels commented 3 years ago

Hi,

When I use the SeuratWrappers to perform LIGER data integration, I have the following error:

Package MacoskoLab/liger is not yet installed Install now?

1: yes 2: no

When I say yes, he says

Selection: yes Skipping install of 'rliger' from a github remote, the SHA1 (d7718b93) has not changed since last install. Use force = TRUE to force installation Error in loadNamespace(name) : there is no package called ‘liger’

I have installed install_github('MacoskoLab/liger'), but the package can be found under the name "rliger".

Can you help me with this problem?

Thanks a lot!

jw156605 commented 3 years ago

This is correct. The repository name is liger, but the package name after installation is rliger. Just do library(rliger) and everything should work.

— Joshua D. Welch, Ph.D. Assistant Professor Department of Computational Medicine and Bioinformatics Department of Computer Science and Engineering University of Michigan 100 Washtenaw Ave. 2044 Palmer Commons Ann Arbor, MI 48109 734-615-0618

From: edbels @.> Sent: Tuesday, April 6, 2021 7:54 AM To: welch-lab/liger @.> Cc: Subscribed @.***> Subject: [welch-lab/liger] Called from: CheckPackage(package = "MacoskoLab/liger", repository = "github") (#209)

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Hi,

When I use the SeuratWrappers to perform LIGER data integration, I have the following error:

Package MacoskoLab/liger is not yet installed Install now?

1: yes 2: no

When I say yes, he says

Selection: yes Skipping install of 'rliger' from a github remote, the SHA1 (d7718b9https://github.com/welch-lab/liger/commit/d7718b93c8db43c37c669647e0c47ebb50684929) has not changed since last install. Use force = TRUE to force installation Error in loadNamespace(name) : there is no package called ‘liger’

I have installed install_github('MacoskoLab/liger'), but the package can be found under the name "rliger".

Can you help me with this problem?

Thanks a lot!

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cgao90 commented 3 years ago

The seurat-wrapper needs an update on this part because of the change in the package name. I've opened a pull request.

ShanSabri commented 3 years ago

Same issue on my end. A fix for this would be great. Any workaround?

jw156605 commented 3 years ago

Sorry for the inconvenience. We have a pull request with the seurat wrappers package but can't do anything until it's merged. The easiest workaround would be to run the analysis in liger directly. You can export the object from seurat and import it into liger.

ShanSabri commented 3 years ago

Sorry, can you elaborate on how to run the exported object in liger directly?

EDIT: so without using SeuratWrappers. Gotcha thanks!

cgao90 commented 3 years ago

Hi @ShanSabri, You can make the conversion using seuratToLiger function in LIGER.