User: Chirag Parsania

gravatar for Chirag Parsania
Chirag Parsania1.5k
Reputation:
1,520
Status:
Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
16 hours ago
Joined:
4 years, 2 months ago
Email:
c**************@gmail.com

All answered queries can also be found on github https://github.com/cparsania/biostar_queries

 

 

Posts by Chirag Parsania

<prev • 194 results • page 1 of 20 • next >
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Comment: C: Get cDNA sequences from NCBI for given protein IDs
... 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 Parsania1.5k
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Comment: C: GO analysis to ID biological processes in my identified protein list? panther? a
... [ClusterProfiler][1] is one of my favourite. [1]: https://yulab-smu.github.io/clusterProfiler-book/chapter1.html ...
written 8 days ago by Chirag Parsania1.5k
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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 Parsania1.5k
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Comment: C: Get cDNA sequences from NCBI for given protein IDs
... 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 Parsania1.5k
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Comment: C: Get cDNA sequences from NCBI for given protein IDs
... I need cDNA (nt) sequences not protein. ...
written 29 days ago by Chirag Parsania1.5k
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Answer: A: Get cDNA sequences from NCBI for given protein IDs
... 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 Parsania1.5k
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Comment: C: Get cDNA sequences from NCBI for given protein IDs
... Bingo... !! How to give file containing several Ids instead of just one id ...
written 4 weeks ago by Chirag Parsania1.5k
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Comment: C: Get cDNA sequences from NCBI for given protein IDs
... 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 Parsania1.5k
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Comment: C: RSEM_R differential expression and PCA plot
... 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 Parsania1.5k
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Get cDNA sequences from NCBI for given protein IDs
... 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 ...
ncbi cdna proteinid written 4 weeks ago by Chirag Parsania1.5k

Latest awards to Chirag Parsania

Good Question 13 days ago, asked a question that was upvoted at least 5 times. For How to find intron co-ordinates from the gff file?
Scholar 6 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Epic Question 11 weeks ago, created a question with more than 10,000 views. For Z-Score calculation by heatmap.2
Popular Question 3 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 4 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 6 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Scholar 6 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 8 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 8 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Scholar 10 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Scholar 11 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 11 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Guru 11 months ago, received more than 100 upvotes.
Supporter 11 months ago, voted at least 25 times.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.

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