- recipe bioconductor-scpipe
Pipeline for single cell multi-omic data pre-processing
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/scPipe.html
- License:
GPL (>= 2)
- Recipe:
A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.
- package bioconductor-scpipe¶
- versions:
2.2.0-0,2.0.0-0,1.19.0-1,1.19.0-0,1.16.1-0,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-1,2.2.0-0,2.0.0-0,1.19.0-1,1.19.0-0,1.16.1-0,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-1,1.12.0-0,1.10.0-0,1.8.0-0,1.6.0-1,1.4.1-0,1.4.0-0,1.2.1-0,1.0.0-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-annotationdbi:
>=1.64.1,<1.65.0a0- depends bioconductor-basilisk:
>=1.14.0,<1.15.0- depends bioconductor-basilisk:
>=1.14.1,<1.15.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biomart:
>=2.58.0,<2.59.0- depends bioconductor-biomart:
>=2.58.0,<2.59.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-dropletutils:
>=1.22.0,<1.23.0- depends bioconductor-dropletutils:
>=1.22.0,<1.23.0a0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-multiassayexperiment:
>=1.28.0,<1.29.0- depends bioconductor-multiassayexperiment:
>=1.28.0,<1.29.0a0- depends bioconductor-org.hs.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-org.hs.eg.db:
>=3.18.0,<3.19.0a0- depends bioconductor-org.mm.eg.db:
>=3.18.0,<3.19.0- depends bioconductor-org.mm.eg.db:
>=3.18.0,<3.19.0a0- depends bioconductor-rhtslib:
>=2.4.0,<2.5.0- depends bioconductor-rhtslib:
>=2.4.0,<2.5.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends bioconductor-rsubread:
>=2.16.0,<2.17.0- depends bioconductor-rsubread:
>=2.16.0,<2.17.0a0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0a0- 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 bioconductor-zlibbioc:
>=1.48.0,<1.49.0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0a0- 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-data.table:
- depends r-dplyr:
- depends r-flexmix:
- depends r-ggally:
- depends r-ggplot2:
- depends r-glue:
>=1.3.0- depends r-hash:
- depends r-magrittr:
- depends r-mass:
- depends r-matrix:
>=1.5.0- depends r-mclust:
- depends r-purrr:
- depends r-rcpp:
>=0.11.3- depends r-reshape:
- depends r-reticulate:
- depends r-rlang:
- depends r-robustbase:
- depends r-scales:
- depends r-stringr:
- depends r-testthat:
- depends r-tibble:
- depends r-tidyr:
- depends r-vctrs:
>=0.5.2- 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-scpipe and update with:: mamba update bioconductor-scpipe
To create a new environment, run:
mamba create --name myenvname bioconductor-scpipe
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-scpipe:<tag> (see `bioconductor-scpipe/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-scpipe/README.html)
