User: Ark

gravatar for Ark
Ark70
Reputation:
70
Status:
Trusted
Location:
US
Last seen:
1 week ago
Joined:
6 months, 3 weeks ago
Email:
t*****************@gmail.com

Undergraduate bioinformatics student.

Posts by Ark

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Finding Gene Name Synonyms
... Thank you very much Pierre! This was exactly what I was looking for! ...
written 5 weeks ago by Ark70
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Finding Gene Name Synonyms
... Hello again, I was curious if anyone had a nice way of finding the gene synonyms for a list of genes? My genes are currently listed as gene symbols, however, any tool or method to fetch synonyms from any type of ID would be a step in the right direction. Conversions in the reverse direction would a ...
gene R written 5 weeks ago by Ark70 • updated 5 weeks ago by cmdcolin1.1k
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Comment: C: K-means With Many Clusters: Quick-TRANSfer steps exceeded
... Thanks for the link! This looks interesting and I will definitely try it out on my data! ...
written 3 months ago by Ark70
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Comment: C: K-means With Many Clusters: Quick-TRANSfer steps exceeded
... Yes, thank you. That was basically what I assumed my issue was. The solution they proposed for using a different algorithm was not applicable in my case. Also, I do actually want an extreme number of clusters, as I am running some tests that need both very low and very high numbers of clusters. Tha ...
written 3 months ago by Ark70
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Answer: A: K-means With Many Clusters: Quick-TRANSfer steps exceeded
... I have been working with this some more and have come to the conclusion that this particular warning is practically unavoidable when I push the number of clusters as high as I am. From what I have read, with an extreme number of clusters and very similar values among the data (many practically equiv ...
written 3 months ago by Ark70
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K-means With Many Clusters: Quick-TRANSfer steps exceeded
... Hello! I am attempting to run the default kmeans function in RStudio on TPM-normalized and feature-scaled RNA-seq data. I am varying the number of centers I present to kmeans (logarithmically increasing 'k' from 1 - 10,000) but I have hit a snag. I am calling the kmeans function in the following w ...
R kmeans rna-seq written 3 months ago by Ark70 • updated 3 months ago by Chirag Parsania1.3k
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Answer: A: How to "Randomly" Select Genes
... I ran into a problem with both of these methods when you have many clusters, so I wanted to post my fix here just in case anyone finds this thread later. If you have many clusters, it is likely that you will have clusters of the same size. The above methods will group together everything with the s ...
written 3 months ago by Ark70
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Comment: C: Finding Only Protein Coding Genes from Gencode GTF
... I see, that is definitely a better approach than I am currently using. Thanks for the suggestions and the links! ...
written 4 months ago by Ark70
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Comment: C: How to "Randomly" Select Genes
... This is nice also. Looks a bit cleaner. Thanks! ...
written 4 months ago by Ark70
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Comment: C: Finding Only Protein Coding Genes from Gencode GTF
... Thanks for your response Igor! I had not seen that page. Thank you for the link! I will dig through and try to determine which labels are useful for me. Do you have any recommendations on a better way to separate the protein coding genes? I am working in R and currently I am using awk and some reg ...
written 4 months ago by Ark70

Latest awards to Ark

Scholar 11 weeks ago, created an answer that has been accepted. For A: grep whole sequences containing a specific motif in a fasta file
Supporter 3 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: grep whole sequences containing a specific motif in a fasta file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: grep whole sequences containing a specific motif in a fasta file

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