Package Recipe 'r-signac'

recipe r-signac

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis.

Homepage:: https://github.com/timoast/signac
Documentation:: https://satijalab.org/signac
License:: MIT / MIT
Recipe:: /r-signac/meta.yaml
Links:: doi: 10.1016/j.cell.2019.05.031

package r-signac¶

Versions:

1.16.0-1, 1.16.0-0, 1.15.0-0, 1.14.0-2, 1.14.0-1, 1.14.0-0, 1.13.0-1, 1.13.0-0, 1.12.0-0,

1.16.0-1, 1.16.0-0, 1.15.0-0, 1.14.0-2, 1.14.0-1, 1.14.0-0, 1.13.0-1, 1.13.0-0, 1.12.0-0, 1.11.0-0, 1.10.0-2, 1.10.0-1, 1.10.0-0, 1.9.0-2, 1.9.0-1, 1.9.0-0, 1.8.0-1, 1.8.0-0, 1.7.0-1, 1.7.0-0, 1.6.0-1, 1.6.0-0, 1.5.0-1, 1.5.0-0, 1.4.0-0, 1.3.0-0, 1.2.1-1, 1.2.1-0, 1.2.0-0, 1.1.1-1, 1.1.1-0, 1.1.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-genomeinfodb >=1.29.3
on bioconductor-genomeinfodb >=1.46.2,<1.47.0a0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on libgcc >=14
on libstdcxx >=14
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr >=1.0.0
on r-fastmatch
on r-future
on r-future.apply
on r-ggplot2
on r-irlba
on r-matrix
on r-patchwork
on r-pbapply
on r-rcpp
on r-rcpproll
on r-rlang
on r-scales
on r-seuratobject >=5.0.2
on r-stringi
on r-tidyr
on r-tidyselect
on r-vctrs

Additional platforms:

linux-aarch64, osx-arm64

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 r-signac

to add into an existing workspace instead, run:

pixi add r-signac

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 r-signac

Alternatively, to install into a new environment, run:

conda create -n envname r-signac

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/r-signac:<tag>

(see r-signac/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/r-signac/README.html)