biomartr (Q31128): Difference between revisions

@@ description / en / description / en @@
+Genomic Data Retrieval
@@ Property / instance of @@
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@@ Property / CRAN project @@
+biomartr
@@ Property / CRAN project: biomartr / rank @@
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+R
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@@ Property / last update: 2 December 2023 / rank @@
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@@ Property / maintained by @@
+Hajk-Georg Drost
@@ Property / maintained by: Hajk-Georg Drost / rank @@
+Normal rank
@@ Property / description @@
+Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized                way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome                retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL',                 and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database                (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve                functional annotation for genomic loci. In addition, users can download entire databases such                as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',                'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
+Normal rank
@@ Property / author @@
+Hajk-Georg Drost
@@ Property / author: Hajk-Georg Drost / rank @@
+Normal rank
@@ Property / author @@
+Haakon Tjeldnes
@@ Property / author: Haakon Tjeldnes / rank @@
+Normal rank
@@ Property / copyright license @@
+GNU General Public License, version 2.0
@@ Property / copyright license: GNU General Public License, version 2.0 / rank @@
+Normal rank
@@ Property / imports @@
+biomaRt
@@ Property / imports: biomaRt / rank @@
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@@ Property / imports @@
+Biostrings
@@ Property / imports: Biostrings / rank @@
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@@ Property / imports @@
+curl
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@@ Property / imports @@
+tibble
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+software version identifier: ≥ 1.9.4
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+downloader
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+RCurl
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+software version identifier: ≥ 1.95-4.5
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+XML
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+fs
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@@ Property / cites work @@
+BioMart – biological queries made easy
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+NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
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+GenBank
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@@ Property / MaRDI profile type @@
+MaRDI software profile
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@@ Property / depends on software @@
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+https://github.com/cran/biomartr
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@@ Property / Software Heritage ID @@
+swh:1:snp:2dd396b8d2481a1fec5c64de3f4e847836977d63
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+source code repository: https://github.com/cran/biomartr
+point in time: 22 December 2023Timestamp +2023-12-22T00:00:00Z
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@@ links / mardi / name / links / mardi / name @@
+Software:31128

Latest revision as of 18:22, 21 March 2024

Genomic Data Retrieval

Language	Label	Description	Also known as
English	biomartr	Genomic Data Retrieval

Statements

instance of

R package

0 references

software version identifier

1.0.2

publication date

23 February 2022

0 references

1.0.3

publication date

7 May 2023

0 references

0.0.1

publication date

22 July 2015

0 references

0.0.2

publication date

7 August 2015

0 references

0.0.3

publication date

2 March 2016

0 references

0.1.0

publication date

7 August 2016

0 references

0.2.0

publication date

22 November 2016

0 references

0.2.1

publication date

15 December 2016

0 references

0.3.0

publication date

9 February 2017

0 references

0.4.0

publication date

14 March 2017

0 references

0.5.1

publication date

28 May 2017

0 references

0.5.2

publication date

20 September 2017

0 references

0.7.0

publication date

3 January 2018

0 references

0.8.0

publication date

27 June 2018

0 references

0.9.0

publication date

21 May 2019

0 references

0.9.1

publication date

10 December 2019

0 references

0.9.2

publication date

11 January 2020

0 references

1.0.4

publication date

20 June 2023

0 references

1.0.5

publication date

4 October 2023

0 references

1.0.6

publication date

24 October 2023

0 references

1.0.7

publication date

2 December 2023

0 references

programmed in

R

0 references

last update

2 December 2023

0 references

maintained by

Hajk-Georg Drost

0 references

description

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.

0 references

0 references

0 references

GNU General Public License, version 2.0

0 references

imports

biomaRt

0 references