recipe bioconductor-scifer

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences






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

(downloads) docker_bioconductor-scifer



depends bioconductor-biostrings:


depends bioconductor-decipher:


depends bioconductor-flowcore:


depends bioconductor-sangerseqr:


depends r-base:


depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-gridextra:

depends r-kableextra:

depends r-knitr:

depends r-plyr:

depends r-rlang:

depends r-rmarkdown:

depends r-scales:

depends r-stringr:

depends r-tibble:



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-scifer

and update with::

   mamba update bioconductor-scifer

To create a new environment, run:

mamba create --name myenvname bioconductor-scifer

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-scifer/tags`_ for valid values for ``<tag>``)

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