User: magicpants

gravatar for magicpants
magicpants60
Reputation:
60
Status:
Trusted
Location:
Last seen:
1 week, 1 day ago
Joined:
2 years ago
Email:
z********@gmail.com

Posts by magicpants

<prev • 24 results • page 2 of 3 • next >
0
votes
2
answers
574
views
2
answers
Comment: C: What kind of read counts of RNA-seq should be used in machine learning models?
... Thanks for the reminder, but what should be removed priorly for highly correlated data? ...
written 9 months ago by magicpants60
1
vote
0
answers
369
views
0
answers
Comment: C: rsID and its link with disease/traits/phenotype
... You can just simply type your question title on google then find some links like this: https://preview.ncbi.nlm.nih.gov/guide/howto/find-human-variations-with-phenotype/ or just to google the rsIDs that you are interested in, also Ensembl biomart is worth exploring. For a bunch of IDs, using tools ...
written 9 months ago by magicpants60
1
vote
2
answers
574
views
2
answers
Answer: A: What kind of read counts of RNA-seq should be used in machine learning models?
... I found the posts: [FPKM or rlog from DEseq2 for machine learning analysis][1] [Log expression for machine learning input][2] The cross-sample normalized log counts were recommended for downstream machine learning techniques, however I need to add the counts of sets of genes as features, maybe I ...
written 9 months ago by magicpants60
2
votes
2
answers
574
views
2
answers
What kind of unit of RNA-seq should be used in machine learning models?
... I want to train a binary classifier using cancer RNA-seq data. After differential expression analysis, I selected some top DEGs as features for glmnet training, however the performances were quite bad, I think this may be due to tumor heterogeneity. Therefore I plan to do feature engineering, like ...
machine learning rna-seq counts written 9 months ago by magicpants60
0
votes
1
answer
622
views
1
answers
Comment: C: How to retrieve Ensembl phenotype data associated with Ensembl variations using
... Thank you so much Ben, I will know better next time ...
written 22 months ago by magicpants60
5
votes
1
answer
622
views
1
answer
How to retrieve Ensembl phenotype data associated with Ensembl variations using Perl API
... I have retrieved all variants in a single chromosome using the slice adapter and variation feature adaptor, then I got a file that contains variant ids and other basic information, looks like: rs867361848 A/G 10010 10010 SNV dbSNP rs370048753 A/T 10014 10014 SNV ...
ensembl perl api written 22 months ago by magicpants60 • updated 22 months ago by Ben_Ensembl1.0k
0
votes
1
answer
789
views
1
answers
Comment: C: What cause the differences between genes annotations from different databases?
... So other databases will contain all official gene symbols and names from HGNC and add their specific annotations? ...
written 23 months ago by magicpants60
8
votes
1
answer
789
views
1
answer
What cause the differences between genes annotations from different databases?
... I want to get the information of all genes on human Y chromosome, then I found the statistics in different databases --Ensembl (GENCODE), NCBI, HGNC -- are dissimilar. For example, protein-coding genes numbers: CCDS 63 HGNC 45 Ensembl 63 NCBI 73 So what leads to these number be different? B ...
gene database next-gen written 23 months ago by magicpants60 • updated 23 months ago by Jean-Karim Heriche20k
0
votes
1
answer
2.1k
views
1
answers
Comment: C: Intersect vcf file and bed file
... I added a header but the same error raised ...
written 2.1 years ago by magicpants60
0
votes
1
answer
2.1k
views
1
answers
Comment: C: Intersect vcf file and bed file
... I tried this command but it only created an empty bed file... ...
written 2.1 years ago by magicpants60

Latest awards to magicpants

Scholar 5 weeks ago, created an answer that has been accepted. For A: Is there a way to get the name or IDs of genes with the goseq table?
Scholar 7 months ago, created an answer that has been accepted. For A: Is there a way to get the name or IDs of genes with the goseq table?
Popular Question 16 months ago, created a question with more than 1,000 views. For Intersect vcf file and bed file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1170 users visited in the last hour