qiime2 | Official repository for the QIIME 2 framework | Genomics library

by qiime2 Python Version: 2017.2.0 License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | qiime2 Summary

qiime2 is a Python library typically used in Artificial Intelligence, Genomics applications. qiime2 has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Source code repository for the QIIME 2 framework. QIIME 2 is a powerful, extensible, and decentralized microbiome bioinformatics platform that is free, open source, and community developed. With a focus on data and analysis transparency, QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. Visit to learn more about the QIIME 2 project.

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Quality

Security

License

Reuse

Support

qiime2 has a low active ecosystem.

It has 394 star(s) with 212 fork(s). There are 39 watchers for this library.

It had no major release in the last 12 months.

There are 112 open issues and 212 have been closed. On average issues are closed in 245 days. There are 5 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of qiime2 is 2017.2.0

Quality

qiime2 has 0 bugs and 0 code smells.

Security

qiime2 has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

qiime2 code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

qiime2 is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

qiime2 releases are available to install and integrate.

Build file is available. You can build the component from source.

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

qiime2 saves you 2796 person hours of effort in developing the same functionality from scratch.

It has 6050 lines of code, 778 functions and 72 files.

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

Top functions reviewed by kandi - BETA

kandi has reviewed qiime2 and discovered the below as its top functions. This is intended to give you an instant insight into qiime2 implemented functionality, and help decide if they suit your requirements.

Return a setuptools cmdclass instance
Handle GET request
Extract the version information
Get the project root directory
Construct a ConfigParser from the given root
Execute action
Define a usage variable
Create a usage variable
Parse a callable signature
Ensure x is a tuple
Imports a given artifact
Wrapper for callable_callable
Validate an index
Save the key to the data store
Remove key
View an artifact as a Metadata
Execute the callable callable
Scans the given setup py py file
Create versioneer config file
Extract the versions of the VCS
Import an artifact from a format
Remove artifact from the repository
Merge one or more metadata
Get a metadata column
Load a Metadata from a file
Save the ref
Returns a temporary path to a temporary file

Get all kandi verified functions for this library.

qiime2 Key Features

No Key Features are available at this moment for qiime2.

qiime2 Examples and Code Snippets

No Code Snippets are available at this moment for qiime2.

Community Discussions

Trending Discussions on qiime2

Phylo tree has no branch lengths using phylosig () R

How to extract the same data from different files

Error: Aesthetics must be either length 1 or the same as the data (9): size

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

Perl module depends on a binary, why tests fail on FreeBSD even if using CheckBin?

QUESTION

Phylo tree has no branch lengths using phylosig () R

Asked 2022-Jan-25 at 12:24

I am having a hard time understanding why my phylo tree (imported as a phyloseq object from QIIME2) appears to have no branch lengths when used in phylosig(). I am trying to compute the phylogenetic signal of my 16S dataset compared to a single continuous metadata variable. All example datasets are included at the bottom of this question.

...

ANSWER

Answered 2022-Jan-25 at 12:24

The problem is not the lack of branch lengths in the tree. What the error message is saying is that the tree does not have the tips that correspond to the names of values in the trait variable. glacialpath must be a named vector and the names must be present in the phylogeny.

In general, a good practice is to check for possible problems in these three areas.

phylo is not a correct phylo format.
phylo should contain tips with names corresponding to those in the metadata.
Related to #2, glacialpath lacks names.

phylo is not a correct phylo format

phytools::phylosig requires that the tree is in correct phylo format. Try to explore the tree with str(phylo), and see whether all values in phylo$edge.length are numeric and there are no missing values.

phylo should contain tips with names corresponding to those in the metadata

What are the samples the phylogenetic signal should be calculated for? Assuming that the column sample in the metadata contains names, reduce the tree to the size of the available data:

Source https://stackoverflow.com/questions/70571914

QUESTION

How to extract the same data from different files

Asked 2021-Apr-16 at 08:36

In order to extract a frecuency table from a qiime2 artifact and write It to a tsv output you have to:

...

ANSWER

Answered 2021-Apr-16 at 08:36

You can write a function and apply it to each file using lapply :

Source https://stackoverflow.com/questions/67121663

QUESTION

Error: Aesthetics must be either length 1 or the same as the data (9): size

Asked 2021-Jan-15 at 09:09

Im trying to plot my PCOA with qiime2R and ggplot2 since I find 2D UniFrac plots more informative than those given with Emperor in 3D. So I followed the qiime2R tutorial, but Im having trouble adding different aesthetics, I have seen other post but I don’t really understand the issue. Here’s my code.

The folks from the qiime2 forum could´t help me, so perhaps you can.

...

ANSWER

Answered 2021-Jan-15 at 09:09

For your updated question:

You are providing two shape values (16 and 1) for Origen, but Origen has 3 values (Minas ..., Rio ..., and Balsas...). You must provide a shape value for each Origen value.

Source https://stackoverflow.com/questions/65732885

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

Perl module depends on a binary, why tests fail on FreeBSD even if using CheckBin?

Asked 2020-Jan-30 at 16:24

I'm made a Perl module (Qiime2::Artifact) that heavily relies on the 'unzip' binary to work[1].

The module's here: https://metacpan.org/pod/Qiime2::Artifact

To declare the dependency I used the CheckBin plugin for Distzilla:

...

ANSWER

Answered 2020-Jan-30 at 16:24

With the precious hints received from you all (special thanks to @Grinnz), it appears that:

unzip is commonly found in BSD but a different flavor ships
CheckBin was indeed working, it's just the binary itself behaving in an unexpected way (specifically exiting with non-zero status if invoked, quite annoying even if not unseen I must say)

Final comment: - Archive::Zip is a good hint, but I will not adopt it as Alien modules are getting harder to install under MacOS. I might change my mind and just put them in miniconda that greatly helps in sorting this problem out.

Source https://stackoverflow.com/questions/59944250

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

Vulnerabilities

No vulnerabilities reported

Install qiime2

Detailed instructions are available in the documentation.

Support

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