recipe snakealtpromoter

A comprehensive pipeline for differential alternative promoter analysis.

Homepage:

https://github.com/YidanSunResearchLab/SnakeAltPromoter

License:

MIT / MIT

Recipe:

/snakealtpromoter/meta.yaml

SnakeAltPromoter is a Snakemake-based pipeline for streamlined, reproducible, and scalable analysis of alternative promoter usage from RNA-seq or CAGE data. It integrates all major steps—from raw read preprocessing to promoter-level quantification and differential analysis—using state-of-the-art tools.

package snakealtpromoter

versions:

1.0.5-0

depends pandas:

depends pyarrow:

depends python:

>=3.11

depends snakemake:

depends streamlit:

requirements:

additional platforms:

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 snakealtpromoter

and update with::

   mamba update snakealtpromoter

To create a new environment, run:

mamba create --name myenvname snakealtpromoter

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 quay.io/biocontainers/snakealtpromoter:<tag>

(see `snakealtpromoter/tags`_ for valid values for ``<tag>``)

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