bambu | guided transcript discovery and quantification | Genomics library

by GoekeLab R Version: v2.0.0 License: GPL-3.0

X-Ray Key Features Code Snippets(3)Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | bambu Summary

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

bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

Support

Quality

Security

License

Reuse

Support

bambu has a low active ecosystem.

It has 107 star(s) with 19 fork(s). There are 5 watchers for this library.

It had no major release in the last 12 months.

There are 12 open issues and 117 have been closed. On average issues are closed in 23 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of bambu is v2.0.0

Quality

bambu has no bugs reported.

Security

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

License

bambu 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

bambu releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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bambu Key Features

No Key Features are available at this moment for bambu.

bambu Examples and Code Snippets

General Usage

Lines of Code : 14

License : Strong Copyleft (GPL-3.0)

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test.bam <- system.file("extdata", "SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam", package = "bambu")
  
fa.file <- system.file("extdata", "Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa", package = "bambu")

gtf.file

Complementary functions

Lines of Code : 11

License : Strong Copyleft (GPL-3.0)

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transcriptToGeneExpression(se)

plotBambu(se, type = "annotation", gene_id)

plotBambu(se, type = "annotation", transcript_id)

plotBambu(se, type = "heatmap") # heatmap 

plotBambu(se, type = "pca") # PCA visualization

plotBambu(se, type = "heatmap

Advanced Options

Lines of Code : 6

License : Strong Copyleft (GPL-3.0)

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bambu(reads, annotations, genome, opt.discovery = list(min.readCount = 5))

bambu(reads, annotations, genome, opt.discovery = list(min.sampleNumber = 5))

bambu(reads, annotations, genome, opt.discovery = list(min.readFractionByGene = 0.1))

bambu(re

Community Discussions

Trending Discussions on bambu

How to filter objects in a array based on the properties

Add current time and change json structure data python

How to filter a data.frame by matching a character string?

Android login and get json array

Scrapy Python response.css loop

QUESTION

How to filter objects in a array based on the properties

Asked 2020-Dec-08 at 17:53

How can i filter objects in a array based on the objects properties?

I have this code right now:

...

ANSWER

Answered 2020-Dec-08 at 17:53

You could filter with a Set for seen title.

Source https://stackoverflow.com/questions/65204151

QUESTION

Add current time and change json structure data python

Asked 2020-Nov-24 at 15:59

So I have exported result from scraping news portal which I stored it to DataFrame, then I export it to csv and json. The scraping, export to csv got no problem, and technically got no problem export it to json too. Here is the result in json files:

...

ANSWER

Answered 2020-Nov-24 at 15:59

Get current time

Source https://stackoverflow.com/questions/64924122

QUESTION

How to filter a data.frame by matching a character string?

Asked 2020-Jul-08 at 17:11

I have those structures:

...

ANSWER

Answered 2020-Jul-07 at 22:59

Using the solution from this answer.

Source https://stackoverflow.com/questions/62784381

QUESTION

Android login and get json array

Asked 2019-Feb-13 at 05:44

i made app that get json array from api using volley, json array will show when login is success.

here are my json response.

...

ANSWER

Answered 2019-Feb-13 at 03:47

you are providing null list on adapter

Source https://stackoverflow.com/questions/54662040

QUESTION

Scrapy Python response.css loop

Asked 2018-Sep-25 at 13:52

I am trying to loop every offer on this website:

...

ANSWER

Answered 2018-Aug-23 at 02:35

Scrapy selector docs. You're using css so we'll stick with that.

The reponse.css() selection is yielding a single element list, because there is only one #offerPage (id's are unique). So you're for loop in parse() is only executing once, but the selector in it is yielding a list with many elements, because there are many h3 > a elements in your first selection.

You should drill into the elements one more level so that the response.css() yields more than one element for your parse() loop. Then iterate through.

Source https://stackoverflow.com/questions/51973028

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

Vulnerabilities

No vulnerabilities reported

Install bambu

You can install bambu from bioconductor:.

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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