recipe slamdunk

Slamdunk is a software tool for SLAMseq data analysis.

Homepage

http://t-neumann.github.io/slamdunk

Documentation

http://t-neumann.github.io/slamdunk/docs.html

Developer docs

https://github.com/t-neumann/slamdunk

License

AGPL / GNU Affero General Public License v3 (AGPLv3)

Recipe

/slamdunk/meta.yaml

Links

doi: 10.1186/s12859-019-2849-7

<img src="http://t-neumann.github.io/slamdunk/images/slamdunk_logo_light.png" width="300" title="Slamdunk">

### Streamlining SLAM-Seq analysis with ultra-high sensitivity.

[](https://github.com/t-neumann/slamdunk/releases/latest) [](https://travis-ci.org/t-neumann/slamdunk)

[](https://hub.docker.com/r/tobneu/slamdunk) [](https://hub.docker.com/r/tobneu/slamdunk/builds/)

[](http://bioconda.github.io/recipes/slamdunk/README.html) [](https://anaconda.org/bioconda/slamdunk) [](https://anaconda.org/bioconda/slamdunk)

[](https://pypi.python.org/pypi/slamdunk) 

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### Slamdunk documentation

http://t-neumann.github.io/slamdunk

### Please cite

Neumann, T., Herzog, V. A., Muhar, M., Haeseler, von, A., Zuber, J., Ameres, S. L., & Rescheneder, P. (2019). [Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2849-7). BMC Bioinformatics, 20(1), 258. http://doi.org/10.1186/s12859-019-2849-7

package slamdunk

Versions

0.4.3-0,  0.4.2-1,  0.4.2-0,  0.4.1-0,  0.4.0-1,  0.4.0-0,  0.3.4-1,  0.3.4-0,  0.3.3-0, 

0.4.3-0,  0.4.2-1,  0.4.2-0,  0.4.1-0,  0.4.0-1,  0.4.0-0,  0.3.4-1,  0.3.4-0,  0.3.3-0,  0.3.2-1,  0.3.2-0

Depends

• biopython >=1.74

• intervaltree >=3.0.2

• joblib >=0.14.0

• nextgenmap 0.5.5.*

• pandas >=0.25.3

• pybedtools >=0.8.0

• python >=3

• r-getopt

• r-gridextra

• r-matrixstats >=0.55.0

• r-tidyverse >=1.3.0

• samtools >=1.9

• varscan 2.4.4.*

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install slamdunk

and update with:

conda update slamdunk

or use the docker container:

docker pull quay.io/biocontainers/slamdunk:<tag>

(see slamdunk/tags for valid values for <tag>)

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/slamdunk/README.html)