Package Recipe 'bioconductor-blase'

recipe bioconductor-blase

Bulk Linking Analysis for Single-cell Experiments

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/blase.html
License:: GPL (>= 3)
Recipe:: /bioconductor-blase/meta.yaml

BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to "date" bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments.

package bioconductor-blase¶

Versions:

1.0.0-0

Depends:

on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-boot
on r-dplyr
on r-ggplot2
on r-matrix
on r-mgcv
on r-patchwork
on r-rlang
on r-seurat >=4.0.0
on r-viridis

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-blase

to add into an existing workspace instead, run:

pixi add bioconductor-blase

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-blase

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-blase

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-blase:<tag>

(see bioconductor-blase/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-blase/README.html)