User: ammasakshay

gravatar for ammasakshay
ammasakshay30
Reputation:
30
Status:
New User
Location:
Last seen:
1 week, 4 days ago
Joined:
4 years, 12 months ago
Email:
a**********@gmail.com

Posts by ammasakshay

<prev • 7 results • page 1 of 1 • next >
0
votes
0
answers
54
views
0
answers
CATALYST - Debarcoding visualisation error
... I'm Using the code found here - http://bioconductor.org/packages/release//bioc/vignettes/CATALYST/inst/doc/preprocessing.html#plotmahal-all-barcode-biaxial-plot My debarcoding script looks like ``` #debarcode sce <- assignPrelim(sce, mat) # view barcode channels rowname ...
R written 12 days ago by ammasakshay30
0
votes
1
answer
1.7k
views
1
answers
Comment: C: How do I extract genes from a KEGG pathway
... Thank you. I'm a little new to this interface. ...
written 23 months ago by ammasakshay30
2
votes
1
answer
1.7k
views
1
answers
Answer: A: How do I extract genes from a KEGG pathway
... I ended up solving it myself. Hopefully this helps anyone who has a similar need. library("KEGGREST") #Get the list of numbers, gene symbols and gene description names <- keggGet("hsa05215")[[1]]$GENE #Delete the gene number by deleting every other line namesodd <- n ...
written 23 months ago by ammasakshay30 • updated 23 months ago by WouterDeCoster45k
0
votes
1
answer
1.7k
views
1
answers
Comment: C: How do I extract genes from a KEGG pathway
... This doesn't help. This is only for genes and does not give us the gene list in pathways. Try your solution with hsa05215 pathway and you will see it does not return the list of 90+ genes. ...
written 23 months ago by ammasakshay30
0
votes
1
answer
1.7k
views
1
answers
Comment: C: How do I extract genes from a KEGG pathway
... I did that here, http://rest.kegg.jp/get/hsa05215 and the gene list is similar to the one i got through R. It has a number gene symbol and description on each line. I want the gene symbol alone. The output under gene looks like this: 1027 CDKN1B; cyclin dependent kinase inhibitor 1B [KO ...
written 23 months ago by ammasakshay30
4
votes
1
answer
1.7k
views
1
answer
How do I extract genes from a KEGG pathway
... Using R I want to generate a list of genes only (without the accompanying text) from a pathway. For example. If the input pathway is [KEGG prostate cancer](https://www.genome.jp/dbget-bin/www_bget?hsa05215), I want my output to be a .csv list of the genes in that pathway. I tried: library("KE ...
gene R bioconductor written 23 months ago by ammasakshay30
0
votes
1
answer
823
views
1
answer
Protein Id mapping at isoform level
... Hello. I would like to write a small program mapping swissprot protein to the refeq protein id to the uniprot id at the isoform level in python. The same genome has different ids in these databases and I spend a lot of time trying to match the proteins between databases. Any help is appreciated. ...
sequence written 5.0 years ago by ammasakshay30 • updated 5.0 years ago by Jean-Karim Heriche24k

Latest awards to ammasakshay

Popular Question 23 months ago, created a question with more than 1,000 views. For How do I extract genes from a KEGG pathway
Scholar 23 months ago, created an answer that has been accepted. For A: How do I extract genes from a KEGG pathway

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 975 users visited in the last hour
_