recipe ourotools

A comprehensive toolkit for quality control and analysis of single-cell long-read RNA-seq data

Homepage:

https://github.com/ahs2202/ouro-tools

Documentation:

https://pypi.org/project/ourotools/

License:

MIT / MIT

Recipe:

/ourotools/meta.yaml

Ouro-Tools is a novel, comprehensive computational pipeline for long-read scRNA-seq with the following key features. Ouro-Tools (1) normalizes mRNA size distributions and (2) detects mRNA 7-methylguanosine caps to integrate multiple single-cell long-read RNA-sequencing experiments across modalities and characterize full-length transcripts, respectively.

package ourotools

versions:

0.2.8-0,  0.2.7-0

depends bitarray:

>=2.5.1

depends h5py:

>=3.8.0

depends intervaltree:

>=3.1.0

depends joblib:

>=1.2.0

depends mappy:

>=2.24

depends matplotlib-base:

>=3.5.2

depends minimap2:

>=2.28

depends nest-asyncio:

>=1.5.6

depends numpy:

>=1.26.4

depends owlready2:

>=0.46

depends pandas:

>=1.5.2

depends plotly:

>=5.18.0

depends pybigwig:

>=0.3.22

depends pysam:

>=0.18.0

depends python:

>=3.11

depends regex:

>=2.5.135

depends samtools:

>=1.10

depends scanpy:

>=1.10.2

depends scipy:

>=1.9.1

depends tqdm:

>=4.64.1

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 ourotools

and update with::

   mamba update ourotools

To create a new environment, run:

mamba create --name myenvname ourotools

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/ourotools:<tag>

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

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