- recipe bioconductor-tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysis
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/tximport.html
- License:
LGPL (>=2)
- Recipe:
- Links:
biotools: tximport
Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.
- package bioconductor-tximport¶
- Versions:
1.38.2-0,1.34.0-0,1.30.0-1,1.30.0-0,1.28.0-0,1.26.0-0,1.22.0-0,1.20.0-0,1.18.0-1,1.38.2-0,1.34.0-0,1.30.0-1,1.30.0-0,1.28.0-0,1.26.0-0,1.22.0-0,1.20.0-0,1.18.0-1,1.18.0-0,1.16.0-0,1.14.0-0,1.12.3-0,1.12.1-1,1.12.1-0,1.12.0-0,1.10.1-0,1.10.0-0,1.8.0-0,1.6.0-0,1.4.0-0,1.0.3-1,1.0.3-0- Depends:
on r-base
>=4.5,<4.6.0a0
- 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-tximport
to add into an existing workspace instead, run:
pixi add bioconductor-tximport
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-tximport
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-tximport
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-tximport:<tag>
(see bioconductor-tximport/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-tximport/README.html)
