- recipe bioconductor-rifi
'rifi' analyses data from rifampicin time series created by microarray or RNAseq
- Homepage:
- License:
GPL-3 + file LICENSE
- Recipe:
'rifi' analyses data from rifampicin time series created by microarray or RNAseq. 'rifi' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, 'rifi' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.
- package bioconductor-rifi¶
- Versions:
1.14.0-0,1.10.0-0,1.6.0-0,1.4.1-0,1.2.0-0- Depends:
on bioconductor-rtracklayer
>=1.70.0,<1.71.0on bioconductor-s4vectors
>=0.48.0,<0.49.0on bioconductor-summarizedexperiment
>=1.40.0,<1.41.0on r-base
>=4.5,<4.6.0a0on r-car
on r-cowplot
on r-domc
on r-dplyr
on r-egg
on r-foreach
on r-ggplot2
on r-nls2
on r-nnet
on r-reshape2
on r-rlang
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-rifi
to add into an existing workspace instead, run:
pixi add bioconductor-rifi
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-rifi
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-rifi
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-rifi:<tag>
(see bioconductor-rifi/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:
[](http://bioconda.github.io/recipes/bioconductor-rifi/README.html)
