samsa2 | SAMSA pipeline , version | Continous Integration library

by transcript R Version: 2.2.01 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | samsa2 Summary

samsa2 is a R library typically used in Devops, Continous Integration applications. samsa2 has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

If you use SAMSA2, please cite the following paper:. Westreich, S.T., Treiber, M.L., Mills, D.A. et al. SAMSA2: a standalone metatranscriptome analysis pipeline. BMC Bioinformatics 19, 175 (2018) doi:10.1186/s12859-018-2189-z.

Support

Quality

Security

License

Reuse

Support

samsa2 has a low active ecosystem.

It has 34 star(s) with 22 fork(s). There are 3 watchers for this library.

It had no major release in the last 12 months.

There are 13 open issues and 41 have been closed. On average issues are closed in 11 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of samsa2 is 2.2.01

Quality

samsa2 has 0 bugs and 0 code smells.

Security

samsa2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

samsa2 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

samsa2 is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

samsa2 releases are available to install and integrate.

Installation instructions are available. Examples and code snippets are not available.

It has 1245 lines of code, 13 functions and 13 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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samsa2 Key Features

No Key Features are available at this moment for samsa2.

samsa2 Examples and Code Snippets

No Code Snippets are available at this moment for samsa2.

Community Discussions

Trending Discussions on samsa2

R: right input directory loads empty input.files and count.table

QUESTION

R: right input directory loads empty input.files and count.table

Asked 2019-Feb-28 at 17:49

I am trying to load multiple .tsv files and then combine the list of tables into one data frame. Working on the right directory

...

ANSWER

Answered 2019-Feb-28 at 17:49

Does something like this work:

Source https://stackoverflow.com/questions/54931292

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install samsa2

Download SAMSA2: git clone https://github.com/transcript/samsa2.git. Either install the dependencies from the links above, or use the setup_and_test/package_installation.bash script provided with SAMSA2 for installing from the included binaries. Access the full databases by downloading them using the full\_database\_download.bash script, located in the setup\_and\_test folder. This downloads the full RefSeq bacteria database, for organism and specific functional results, and the SEED Subsystems database, which is used for hierarchical functional ontology. Make changes to the master_script.bash, which performs the first 3 of 4 steps in the SAMSA2 pipeline (preprocessing, annotation, aggregation). If not using master_script, use DIAMOND to annotate your reads against a database of your choosing (note that database must be local and DIAMOND-indexed). See "example\_DIAMOND\_annotation\_script.bash" for more details. If not using master_script, use "DIAMOND\_analysis\_counter.py" to create a ranked abundance summary of the DIAMOND results from each metatransciptome file. Import these abundance summaries into R and use "run\_DESeq\_stats.R" to determine the most significantly differing features between either individual metatranscriptomes, or control vs. experimental groups.
Download SAMSA2: git clone https://github.com/transcript/samsa2.git
Either install the dependencies from the links above, or use the setup_and_test/package_installation.bash script provided with SAMSA2 for installing from the included binaries.
Access the full databases by downloading them using the full\_database\_download.bash script, located in the setup\_and\_test folder. This downloads the full RefSeq bacteria database, for organism and specific functional results, and the SEED Subsystems database, which is used for hierarchical functional ontology.
Make changes to the master_script.bash, which performs the first 3 of 4 steps in the SAMSA2 pipeline (preprocessing, annotation, aggregation)
If not using master_script, use DIAMOND to annotate your reads against a database of your choosing (note that database must be local and DIAMOND-indexed). See "example\_DIAMOND\_annotation\_script.bash" for more details.
If not using master_script, use "DIAMOND\_analysis\_counter.py" to create a ranked abundance summary of the DIAMOND results from each metatransciptome file.
Import these abundance summaries into R and use "run\_DESeq\_stats.R" to determine the most significantly differing features between either individual metatranscriptomes, or control vs. experimental groups.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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