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seamless's Issues

MuSiC API changes broke the package

Hi I wonder if there is anyway to get the underlying SingleCellExperiment now, given MuSiC changed their API, so current ExpressionSet could not be used anymore.

UPDATE: Per users’ requests, we have updated MuSiC functions (version 1.0.0) and SingleCellExperiment objects are used to handle single cell references, where sparse matrices are compatible as read counts.

xuranw/MuSiC@5e7d038

No package called xbioc

I'm trying to follow along with the readme, but I get the following error

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(seAMLess)
> library(xbioc)
Error in library(xbioc) : there is no package called ‘xbioc’

I'm testing in a clean conda environment that only contains r-seamless: environment.zip

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