Package Recipe 'bioconductor-flames' — Bioconda documentation

recipe bioconductor-flames

FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

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

Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

package bioconductor-flames#

Versions:

2.4.2-1, 2.4.2-0, 1.8.0-0, 1.6.0-0, 1.3.4-1, 1.3.4-0, 1.0.2-2, 1.0.2-1, 1.0.2-0,

2.4.2-1, 2.4.2-0, 1.8.0-0, 1.6.0-0, 1.3.4-1, 1.3.4-0, 1.0.2-2, 1.0.2-1, 1.0.2-0, 0.99.31-0

Depends:

on __glibc >=2.17,<3.0.a0
on bioconductor-bambu >=3.12.0,<3.13.0
on bioconductor-bambu >=3.12.1,<3.13.0a0
on bioconductor-basilisk >=1.22.0,<1.23.0
on bioconductor-basilisk >=1.22.0,<1.23.0a0
on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-complexheatmap >=2.26.1,<2.27.0a0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0a0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-ggbio >=1.58.0,<1.59.0
on bioconductor-ggbio >=1.58.0,<1.59.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0
on bioconductor-matrixgenerics >=1.22.0,<1.23.0a0
on bioconductor-rhtslib >=3.6.0,<3.7.0
on bioconductor-rhtslib >=3.6.0,<3.7.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-rtracklayer >=1.70.1,<1.71.0a0
on bioconductor-s4arrays >=1.10.0,<1.11.0
on bioconductor-s4arrays >=1.10.1,<1.11.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-scater >=1.38.0,<1.39.0
on bioconductor-scater >=1.38.0,<1.39.0a0
on bioconductor-scran >=1.38.0,<1.39.0
on bioconductor-scran >=1.38.0,<1.39.0a0
on bioconductor-scuttle >=1.20.0,<1.21.0
on bioconductor-scuttle >=1.20.0,<1.21.0a0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-seqinfo >=1.0.0,<1.1.0a0
on bioconductor-shortread >=1.68.0,<1.69.0
on bioconductor-shortread >=1.68.0,<1.69.0a0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0
on bioconductor-spatialexperiment >=1.20.0,<1.21.0
on bioconductor-spatialexperiment >=1.20.0,<1.21.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on bzip2 >=1.0.8,<2.0a0
on git
on glpk >=5.0,<6.0a0
on libblas >=3.9.0,<4.0a0
on libcurl >=8.21.0,<9.0a0
on libgcc >=14
on libgfortran
on libgfortran5 >=14.4.0
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.3,<6.0a0
on libstdcxx >=14
on libuv
on libxml2
on libxml2-16 >=2.15.3
on libzlib >=1.3.2,<2.0a0
on minimap2 >=2.29
on ncurses >=6.6,<7.0a0
on oarfish >=0.8,<0.9
on pip
on pkg-config
on python 3.11.9
on r-abind
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-cli
on r-cowplot
on r-crew
on r-dplyr
on r-ggplot2
on r-gridextra
on r-igraph
on r-jsonlite
on r-magick
on r-magrittr
on r-matrix
on r-r.utils
on r-rcolorbrewer
on r-rcpp
on r-readr
on r-reticulate
on r-scatterpie
on r-stringr
on r-testthat
on r-tibble
on r-tidyr
on r-tidyselect
on samtools >=1.14

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-flames

to add into an existing workspace instead, run:

pixi add bioconductor-flames

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-flames

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-flames

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-flames:<tag>

(see bioconductor-flames/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

.. Create all the necessary plots for each package by loading all the correct specs and data. Important points on the place and implementation of this script block: 1. It is here, and not in a separate HTML file, as it needs to have the `package.name` rendered in for each package. 2. All packages are handled in one `window.onload` function, as multiple instances of this throughout a (rendered) HTML just overwrite each other.

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-flames/README.html)