dada2 | Accurate sample inference from amplicon data | Genomics library

by benjjneb R Version: v1.26 License: LGPL-3.0

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | dada2 Summary

dada2 is a R library typically used in Artificial Intelligence, Genomics applications. dada2 has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. You can download it from GitHub.

Exact sample inference from high-throughput amplicon data. Resolves real variants differing by as little as one nucleotide. Visit the DADA2 website for the most detailed and up-to-date documentation.

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Quality

Security

License

Reuse

Support

dada2 has a low active ecosystem.

It has 388 star(s) with 135 fork(s). There are 40 watchers for this library.

It had no major release in the last 12 months.

There are 347 open issues and 1338 have been closed. On average issues are closed in 38 days. There are 6 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of dada2 is v1.26

Quality

dada2 has 0 bugs and 0 code smells.

Security

dada2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

dada2 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

dada2 is licensed under the LGPL-3.0 License. This license is Weak Copyleft.

Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

Reuse

dada2 releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 146 lines of code, 0 functions and 1 files.

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

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dada2 Key Features

No Key Features are available at this moment for dada2.

dada2 Examples and Code Snippets

No Code Snippets are available at this moment for dada2.

Community Discussions

Trending Discussions on dada2

Create a SQL query based on SELECT results

Is it possible to add a conditional statement in snakemake's rule all?

When I press the button back, my application stops working

R session abort when I use assignTaxonomy

QUESTION

Create a SQL query based on SELECT results

Asked 2022-Feb-10 at 16:18

Im used to basic SQL statements only so far, but Im full of Ideas how to realise some tasks.

Hopefully someone is more skilled and could help:

I am about to alter columns types in different tables from TEXT/MEMO to VARCHAR(MAX). There are really a lot of tables needed to be checked and querys to be individually made. BUT, luckily we have an table, which holds that information and gives an overview in which table there are TEXT/MEMO columns.

The result of such an table (WHERE FIELD_TYPE ='M') looks for e.g. like that:

TAB_DESC FIELD_NAME FIELD_TYPE DADA2 REMARKS M DADA3 COMMENT M DADA4 REMARK M

That result means in our system, for e.g. that the Table "TABLE_QQ_DADA2" has a column "REMARKS" which is TEXT/MEMO. Now it needs to be VARCHAR(MAX).

So based on that table I would simply type create manually

...

ANSWER

Answered 2022-Feb-10 at 16:18

further research led me to an answer in that post:

T-SQL loop over query results

I didnt has the right keywords for proper research before. Maybe an Admin can comment that?

Source https://stackoverflow.com/questions/71065958

QUESTION

Is it possible to add a conditional statement in snakemake's rule all?

Asked 2020-Nov-23 at 07:20

I want to run multiple snakefiles called qc.smk , dada2.smk, picrust2.smkusing singularity. Then there is one snakefile called longitudinal.smk I would like to run conditionally. For example, if longitudinal data is being used.

...

ANSWER

Answered 2020-Nov-23 at 07:20

You can define a list (or dict) of what you want as output outside of the rule all, and feed that to the input, something like this works:

Source https://stackoverflow.com/questions/64949149

QUESTION

When I press the button back, my application stops working

Asked 2020-Jul-15 at 21:03

Good afternoon, I have an application that has an activity that is a menu and communicates with 2 other activities (one to choose a name from a list and the other to choose an exercise). The passing of data between the menu and these activities works correctly. The problem I have is that if the user clicks the back button instead of choosing a name from the list, for example, the application stops working and in the logcat I get an error. in the line of the menu activity where I have the getStringExtra ();

If someone knows how to solve it, I would really appreciate it.

This is the code of de menu activity

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ANSWER

Answered 2020-Jul-15 at 21:03

In your onActivutyResult() you have to check if your result code is ok, if someone doesn't select anything it throws back nothing try this:

Source https://stackoverflow.com/questions/62919546

QUESTION

R session abort when I use assignTaxonomy

Asked 2020-Feb-19 at 02:51

I have been having this problem for more than a week now and I am running out of time and patience.This problem occurs when I run my script on a Mac and when I run it on a PC (no difference of results from more RAM, it just aborts faster). When I try to run this line of my dataset, the session aborts.

...

ANSWER

Answered 2020-Feb-19 at 02:51

This is probably caused by a bug that was introduced in 1.14, see the Github issue here for more information: https://github.com/benjjneb/dada2/issues/916

We've just identified the cause, and a fix should be out soon. For immediate use, the workaround is to turn off multithreading, or to revert to the previous release 1.12.

Source https://stackoverflow.com/questions/60282755

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

Vulnerabilities

No vulnerabilities reported

Install dada2

The dada2 package binaries are available through Bioconductor:. In order to install dada2 from source (and get the latest and greatest new features) see our installation from source instructions.

Support

The tutorial walkthrough of the DADA2 pipeline on paired end Illumina Miseq data. The dada2 R package manual. Further documentation is available on the DADA2 front page.

Find more information at: