User: Chirag Parsania
Chirag Parsania • 1.5k
- Reputation:
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- Location:
- University of Macau
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- Google Scholar Page
- Last seen:
- 16 hours ago
- Joined:
- 4 years, 2 months ago
- Email:
- c**************@gmail.com
Posts by Chirag Parsania
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... I wrote complete solution [here][1] in step by step manner
[1]: http://rpubs.com/parsaniac/ncbi_protein_id_to_cds ...
written 8 days ago by
Chirag Parsania • 1.5k
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... [ClusterProfiler][1] is one of my favourite.
[1]: https://yulab-smu.github.io/clusterProfiler-book/chapter1.html ...
written 8 days ago by
Chirag Parsania • 1.5k
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Comment:
C: Metabolic pathway Mapping
... One way to map KEGG pathway is using [KEGG mapper][1]
[1]: https://www.genome.jp/kegg/tool/map_pathway2.html ...
written 14 days ago by
Chirag Parsania • 1.5k
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... yes, I got from @Sej's answer. However, its partial solution as we further need to filter `all_cds.fasta`. And that's what I mentioned in the Rscript. ...
written 29 days ago by
Chirag Parsania • 1.5k
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... I need cDNA (nt) sequences not protein. ...
written 29 days ago by
Chirag Parsania • 1.5k
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... Once `all_cds.fasta` downloaded as mentioned above by @SejModha, below is the R script to get the query sequences.
library(tidyverse)
## ncbi query protein ids for which we need cDNA fasta file
query_ids <- c("WP_030938735.1", "WP_073767452.1", "WP_075030623.1", "WP_073737 ...
written 29 days ago by
Chirag Parsania • 1.5k
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... Bingo... !! How to give file containing several Ids instead of just one id
...
written 4 weeks ago by
Chirag Parsania • 1.5k
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... Thanks!
Somehow I got the nucleotide (cDNA) co-ordinates for my query protein id (`Wp_*`). Is there a way to get sequences from NCBI using nucletide co-ordinates ?
Protein `Nucleotide Accession` Start Stop Strand
1 WP_115909503.1 ...
written 4 weeks ago by
Chirag Parsania • 1.5k
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235
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... This is very vague question to answer. It depends on for what purpose you want to plot the heatmap ...
written 4 weeks ago by
Chirag Parsania • 1.5k
3
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... Hi,
I have following NCBI protein ids, which I got from blast result. I want cDNA sequences for all of them. How can I get them. I tried batch entrez but it didn't work
WP_114529907
WP_086161776
WP_023545800
WP_055635421
WP_046726840
WP_019985024
WP_030816474
WP_01 ...
written 4 weeks ago by
Chirag Parsania • 1.5k
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For Z-Score calculation by heatmap.2
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