User: Hajk-Georg Drost

Reputation:
130
Status:
Trusted
Location:
Cambridge
Website:
https://github.com/HajkD
Twitter:
@HajkDrost
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Google Scholar Page
Last seen:
3 days, 17 hours ago
Joined:
1 year, 10 months ago
Email:
h****@cam.ac.uk

Post Doctoral Research Associate in Bioinformatics at the University of Cambridge

Posts by Hajk-Georg Drost

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Download fungal genomes
... I know that this question is already quite old, but I now implemented a new package named [biomartr][1] that can perform bulk retrieval of genomes, proteomes, cds, gff, etc. Since the actual question is "Download fungal genomes" I will provide some [biomartr][2] based examples as a reference for peo ...
written 22 months ago by Hajk-Georg Drost130
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Comment: C: Download All The Bacterial Genomes From Ncbi
... Many thanks for pointing out to me that this functionality might be useful. I sat down and extended the functionality of the meta.retrieval() function which now allows you to specify the "group" argument in addition to the "kingdom" argument. This way, you can download subgroups of species. Unfortun ...
written 22 months ago by Hajk-Georg Drost130
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Answer: A: where can i download ncbi and swissuniprot ftp protein, gene and genome sequence
... I know that this question is already 2 years old, but I hope that my answer might be useful to others anyway. I implemented a standardized way to automate the genome retrieval process in R (see [biomartr][1] package). To retrieve all bacterial reference genomes and corresponding CDS, proteome, and ...
written 22 months ago by Hajk-Georg Drost130
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Answer: A: Download All The Bacterial Genomes From Ncbi
... I know that this question is already 4 years old, but I hope that my answer might be useful to others anyway. I implemented a standardized way to automate the genome retrieval process in R (see [biomartr][1] package). To retrieve all bacterial reference genomes from several database sources one ca ...
written 22 months ago by Hajk-Georg Drost130
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Answer: A: NCBI nr database
... In case you wish to download the NCBI nr or NCBI nt (for nucleotide sequences) databases to your hard drive with the R programming language you can use the [biomartr][1] package. Simply type: # download the entire NCBI nr database biomartr::download.database.all(db = "nr") or # downl ...
written 22 months ago by Hajk-Georg Drost130
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Answer: A: Where can I find genome of a single bacteria?
... I know that this question is already almost 3 years old, but I hope that my answer might be useful to others anyway. I implemented a standardized way to automate the genome retrieval process in R (see [biomartr][1] package). To retrieve a bacterial reference genome from several database sources us ...
written 22 months ago by Hajk-Georg Drost130
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Answer: A: Where Can I Download Human Reference Genome In Fasta Format? Hgref.Fa File
... I know that this question is already 6 years old, but I hope that my answer might be useful to others anyway. I implemented a standardized way to automate the genome retrieval process in R (see [biomartr package][1]). To retrieve the human reference genome from several database sources one can si ...
written 22 months ago by Hajk-Georg Drost130 • updated 3 months ago by RamRS19k
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Comment: C: How To Download Full Genome Sequence
... Oops, that's my bad :) Many thanks for pointing it out to me. I hope that it is useful anyway for people who have similar questions in the future. ...
written 22 months ago by Hajk-Georg Drost130
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Answer: A: How To Download Full Genome Sequence
... Hi, I also struggled to find a standardized way to automate the genome retrieval process for subsequent data analysis or pipelining for genomics studies. So I sat down and wrote an R package named [biomartr][1] to fulfill this task.This way, not every study uses its own home-made shell script to re ...
written 22 months ago by Hajk-Georg Drost130

Latest awards to Hajk-Georg Drost

Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Download All The Bacterial Genomes From Ncbi
Appreciated 18 months ago, created a post with more than 5 votes. For A: Download All The Bacterial Genomes From Ncbi
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Download All The Bacterial Genomes From Ncbi
Autobiographer 22 months ago, has more than 80 characters in the information field of the user's profile.

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