Package Recipe 'bioconductor-scifer'

recipe bioconductor-scifer

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/scifer.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-scifer/meta.yaml

Have you ever index sorted cells in a 96 or 384-well plate and then sequenced using Sanger sequencing? If so, you probably had some struggles to either check the electropherogram of each cell sequenced manually, or when you tried to identify which cell was sorted where after sequencing the plate. Scifer was developed to solve this issue by performing basic quality control of Sanger sequences and merging flow cytometry data from probed single-cell sorted B cells with sequencing data. scifer can export summary tables, 'fasta' files, electropherograms for visual inspection, and generate reports.

package bioconductor-scifer¶

Versions:

1.12.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-basilisk >=1.22.0,<1.23.0
on bioconductor-basilisk.utils >=1.22.0,<1.23.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-decipher >=3.6.0,<3.7.0
on bioconductor-flowcore >=2.22.0,<2.23.0
on bioconductor-pwalign >=1.6.0,<1.7.0
on bioconductor-sangerseqr >=1.46.0,<1.47.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr
on r-ggplot2
on r-gridextra
on r-here
on r-kableextra
on r-knitr
on r-plyr
on r-reticulate
on r-rlang
on r-rmarkdown
on r-scales
on r-stringr
on r-tibble

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-scifer

to add into an existing workspace instead, run:

pixi add bioconductor-scifer

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-scifer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-scifer

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-scifer:<tag>

(see bioconductor-scifer/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-scifer/README.html)