biomaRt | R package providing query functionality to BioMart | Genomics library

by grimbough R Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | biomaRt Summary

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

The package provides an R interface to datasets that provide access via the BioMart software suite.

Support

Quality

Security

License

Reuse

Support

biomaRt has a low active ecosystem.

It has 17 star(s) with 9 fork(s). There are 3 watchers for this library.

It had no major release in the last 6 months.

There are 19 open issues and 36 have been closed. On average issues are closed in 90 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of biomaRt is current.

Quality

biomaRt has no bugs reported.

Security

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

License

biomaRt does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

biomaRt releases are not available. You will need to build from source code and install.

Top functions reviewed by kandi - BETA

kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of biomaRt

Get all kandi verified functions for this library.

biomaRt Key Features

No Key Features are available at this moment for biomaRt.

biomaRt Examples and Code Snippets

No Code Snippets are available at this moment for biomaRt.

Community Discussions

Trending Discussions on biomaRt

biomaRt getBM not working due to getNodeSet {XML} error

ID conversion from Drosophila Gene Symbols to Human Gene Symbols

R biomaRt package: obtaining all values in linked databases

Looping with biomart in R

GenomicFeatures Installation and Loading Error "there is no package called ‘GenomicFeatures" via Python3 rpy2

Trying to convert Ensembl ID to gene name in R (biomaRt)

How can I search and condense repetitive rows in a data frame in R?

My venn diagrams dont intersect - what's missing/wrong with my code

Is there a way to access a specific coding sequence of a gene of interest on ENSEMBL in R?

Internal Server Errors when querying biomart?

QUESTION

biomaRt getBM not working due to getNodeSet {XML} error

Asked 2021-May-31 at 07:45

I'm running the following code in r and it is not working. getBM seems to not work for any arguments. Am I doing something wrong?

...

ANSWER

Answered 2021-May-31 at 07:45

Ensembl is temporarily unavailable according to https://www.ensembl.org/info/.

Source https://stackoverflow.com/questions/67759139

QUESTION

ID conversion from Drosophila Gene Symbols to Human Gene Symbols

Asked 2021-Jan-22 at 16:08

I am looking for an R solution (or a general logic solution) to convert Drosophila melanogaster gene ids into Homo sapiens gene ids. Using R/BiomaRt is problematic, due to the ever-changing nature of the BiomaRt dataset, and its dependence on an internet connection and server status.

The gene ids are in the FlyBase format, but I also have human-friendly gene symbols, e.g.

...

ANSWER

Answered 2021-Jan-22 at 16:08

I think you can use the FlyBase orthologs table, which is periodically updated and also has DIOPT scores for each ortholog: ftp://ftp.flybase.net/releases/current/precomputed_files/orthologs/dmel_human_orthologs_disease_fb_2020_06.tsv.gz

Source https://stackoverflow.com/questions/65848648

QUESTION

R biomaRt package: obtaining all values in linked databases

Asked 2020-Dec-03 at 14:47

A bioinformatics programming question. In R, I have a classic speciesA-to-speciesB gene symbol conversion, in this example from mouse to human, which I'm performing using biomaRt, and specifically the getLDS function.

...

ANSWER

Answered 2020-Dec-03 at 14:47

I believe a workaround could be retrieving all IDs from the Biomart database itself, here: https://www.ensembl.org/biomart/martview/

Click on choose database -> Ensembl Genes
Choose dataset -> your selected species (e.g. Mouse genes)
Click on Results -> Check "Unique results only" -> Go
Profit

The list retrieved here has currently 53605 ids, which is, I believe, what you need.

Enjoy!

Source https://stackoverflow.com/questions/65127646

QUESTION

Looping with biomart in R

Asked 2020-Oct-05 at 05:13

I have a dataset list that I created based on many files.

...

ANSWER

Answered 2020-Oct-05 at 05:13

You are not returning the data frame in the function call.

Source https://stackoverflow.com/questions/64199744

QUESTION

GenomicFeatures Installation and Loading Error "there is no package called ‘GenomicFeatures" via Python3 rpy2

Asked 2020-Aug-28 at 20:32

I am trying to use the Bioconductor GenomicFeatures objects and methods via python rpy2 so when I execute the following code:

...

ANSWER

Answered 2020-Aug-28 at 20:32

Thankfully I was able to fix the issue I was having with the installation and loading of the Bioconductor GenomicFeatures from within python3.8 via rpy2 .I spent hours reaching that solution so I wanted to share the solution of what I did so that if whom end up with the same issue can find it.

Basically, when tracking the error log, it seems that the actual error was pointing to this particular error line:

Source https://stackoverflow.com/questions/63639937

QUESTION

Trying to convert Ensembl ID to gene name in R (biomaRt)

Asked 2020-Jun-22 at 22:14

I have a large dataset of gene expression data and I'm trying to convert the gene identifiers into gene names using biomaRt in RStudio, but for some reason when I use the merge function on my data frames, my entire data table is merged wrong/erased. I've looked at the previous questions here, but no matter what I try, my code doesn't seem to work properly. Thank you infinitely!

...

ANSWER

Answered 2020-Jun-22 at 03:31

If you want to just overwrite the Ensemble IDs with the HGNC IDs you can do it in one step:

Source https://stackoverflow.com/questions/62480055

QUESTION

How can I search and condense repetitive rows in a data frame in R?

Asked 2020-May-11 at 05:39

I'm using R to process RNA sequencing data, to which I'm very new. I'm using data frames of reference material from BioMart which, when GO terms are included, are very badly arranged (as follows).

...

ANSWER

Answered 2020-May-11 at 05:39

Ok - I think something like this might be what you're looking for...

I've made a minimal example dataset - test_data containing some genes & some annotations.

Source https://stackoverflow.com/questions/61697272

QUESTION

My venn diagrams dont intersect - what's missing/wrong with my code

Asked 2020-May-01 at 23:24

I have two lists of genes and i want to represent the overlap between the lists in a venn diagram. Could anybody suggest what I am missing in the code below? I'm using the VennDiagram package and the result i get is two non intersecting circles. I have also used Venny https://bioinfogp.cnb.csic.es/tools/venny/index2.0.2.html to draw the venn and confirmed there is an overlap.

...

ANSWER

Answered 2020-May-01 at 23:24

I have a few remarks on your data:

Source https://stackoverflow.com/questions/61523041

QUESTION

Is there a way to access a specific coding sequence of a gene of interest on ENSEMBL in R?

Asked 2020-Mar-11 at 12:44

I am trying to find a way to retrieve the coding sequence (CDS) of a specific gene of interest and load it into R. I tried my luck with the BioMart package, but it doesn't let me specify which gene I am interested in.

Any help is appreciated!

Best, Heiko

...

ANSWER

Answered 2020-Mar-11 at 12:44

This should work:

Source https://stackoverflow.com/questions/60634006

QUESTION

Internal Server Errors when querying biomart?

Asked 2020-Feb-03 at 05:02

When executing R commands with the biomaRt package, I often get the error "Internal Server Error (HTTP 500)." with basic commands like

...

ANSWER

Answered 2020-Feb-03 at 05:02

I circumvented this by setting mirror argument to "useast". Valid mirror options are 'www', 'uswest', 'useast', 'asia'. If no mirror is specified the primary site at www.ensembl.org will be used (it appears they are overloaded on the primary).

Source https://stackoverflow.com/questions/60032266

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