- recipe bioconductor-lemur
Latent Embedding Multivariate Regression
- Homepage:
- License:
MIT + file LICENSE
- Recipe:
Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.
- package bioconductor-lemur¶
- versions:
1.0.4-0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocneighbors:
>=1.20.0,<1.21.0- depends bioconductor-biocneighbors:
>=1.20.0,<1.21.0a0- depends bioconductor-delayedmatrixstats:
>=1.24.0,<1.25.0- depends bioconductor-delayedmatrixstats:
>=1.24.0,<1.25.0a0- depends bioconductor-glmgampoi:
>=1.14.0,<1.15.0- depends bioconductor-glmgampoi:
>=1.14.0,<1.15.0a0- depends bioconductor-hdf5array:
>=1.30.0,<1.31.0- depends bioconductor-hdf5array:
>=1.30.0,<1.31.0a0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-limma:
>=3.58.1,<3.59.0a0- depends bioconductor-matrixgenerics:
>=1.14.0,<1.15.0- depends bioconductor-matrixgenerics:
>=1.14.0,<1.15.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-singlecellexperiment:
>=1.24.0,<1.25.0- depends bioconductor-singlecellexperiment:
>=1.24.0,<1.25.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-harmony:
- depends r-irlba:
- depends r-matrix:
- depends r-matrixstats:
- depends r-rcpp:
- depends r-rcpparmadillo:
- depends r-rlang:
- depends r-vctrs:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-lemur and update with:: mamba update bioconductor-lemur
To create a new environment, run:
mamba create --name myenvname bioconductor-lemur
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-lemur:<tag> (see `bioconductor-lemur/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-lemur/README.html)
