User: Ahill

gravatar for Ahill
Ahill1.3k
Reputation:
1,270
Status:
Trusted
Location:
United States
Last seen:
13 hours ago
Joined:
7 years, 1 month ago
Email:
h********@gmail.com

Posts by Ahill

<prev • 121 results • page 1 of 13 • next >
0
votes
1
answer
99
views
1
answers
Answer: A: GEO .cel file and the preview table are they the same thing?
... The .cel files are the almost-most-raw intensity data, and contain the probeset-level intensities from the array. So (for example) if there were 11 probe-pairs per probeset on the array, the .cel file would contain 22 intensities per probeset. According to the GEO page you linked, the data table a ...
written 10 days ago by Ahill1.3k
0
votes
1
answer
102
views
1
answers
Answer: A: Query based on PMIDs
... The [NCBI elink utility][1] will take a list of PMIDs as input and map to GEO GDS, or SRA accessions. For example, here are 2 PMIDs that each have one associated GEO GDS: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=gds&id=15772128&id=24808371 This call re ...
written 12 days ago by Ahill1.3k
0
votes
2
answers
328
views
2
answers
Comment: C: How can I contribute to the Bioinformatics community as a Software Engineer
... You could reach out to an open source bioinformatics project that could use experienced developer help. This earlier post had listed a few examples [https://www.biostars.org/p/130126/][1] but I'm sure others can offer many more ideas. [1]: https://www.biostars.org/p/130126/ ...
written 5 weeks ago by Ahill1.3k
1
vote
1
answer
190
views
1
answers
Answer: C: How to do feature selection using PCA?
... It can be valid to use PC scores as the independent variables in linear models, instead of the underlying primary variables. For predicting a binary outcome like disease/healthy, you could look at a lm() logistic model like: disease.status ~ PC1 + PC2 + ... Of course, the usefulness of this w ...
written 5 weeks ago by Ahill1.3k
0
votes
1
answer
190
views
1
answers
Comment: C: How to do feature selection using PCA?
... Are you looking to predict your Target Variable (disease/healthy) from the clinical and genomic data? It sounds like you have labeled training data where the disease/healthy classification is known. If so, you might want to use supervised approaches to do feature selection, rather than unsupervise ...
written 5 weeks ago by Ahill1.3k
1
vote
1
answer
168
views
1
answers
Comment: C: Genome annotation: small dataset of genomes
... If searching for PF00502 domain by BLASTP, you may need to be careful that your hits are true positives for this domain, since the domain has variability. If your 13 genomes are curated in UniProt, and what you need to find is the all the proteins in the genome that match the domain, one alternativ ...
written 6 weeks ago by Ahill1.3k
0
votes
1
answer
197
views
1
answers
Answer: A: Fosmid contamination in C. elegans genome?
... The chromsome X sequence was assembled from genomic DNA fragments that were packaged into fosmids. In this case, your fosmid (FO081428.1) was one of a number of fosmids that were assembled together to form the inferred chromosome X sequence (NC_003284.9). So this is not a contamination - in fact t ...
written 9 weeks ago by Ahill1.3k
1
vote
1
answer
233
views
1
answers
Comment: C: Faster UMI extraction from scRNA-Seq data
... You mentioned you are running on a linux cluster. What job management system are you using? How many fastq files (elements in ${cells[@]})? If more than one,can you simply unroll your for loop, which runs each $cell serially, and execute a set of simultaneous jobs that will run in parallel, one p ...
written 12 weeks ago by Ahill1.3k
0
votes
0
answers
114
views
0
answers
Comment: C: Genes for a specific HPO term. Charite, Monarch initialive or other website ?
... The longer list of 6007 genes shown at the link you provided appears to include multiple other phenotypes and species, and an export filtered to "Homo sapiens" yields 10,396 genes, which makes me question the interpretation of this interface. You may want to query the site owners or their documenta ...
written 12 weeks ago by Ahill1.3k
0
votes
2
answers
180
views
2
answers
Answer: A: How do microarray manufacturers decide on the number of probe pairs in a probese
... I'll add that one consideration driving the number of probe-pairs per probe-set in later Affymetrix designs was the desire to query more transcripts in the same amount of silicon real estate, given the fixed size (in square microns) of each probe feature, which was determined by the resolution of th ...
written 3 months ago by Ahill1.3k

Latest awards to Ahill

Teacher 14 days ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For convert MACH .mlprob to Oxford .gen format
Great Question 11 weeks ago, created a question with more than 5,000 views. For Resources for flow cytometry bioinformatics
Appreciated 3 months ago, created a post with more than 5 votes. For A: Why gene expression data should be log2 transformed?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Why gene expression data should be log2 transformed?
Scholar 7 months ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Voter 9 months ago, voted more than 100 times.
Centurion 9 months ago, created 100 posts.
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Guru 11 months ago, received more than 100 upvotes.
Librarian 15 months ago, created a post with more than 10 bookmarks. For Resources for flow cytometry bioinformatics
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Scholar 21 months ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Prophet 2.1 years ago, created a post with more than 20 followers. For Resources for flow cytometry bioinformatics
Commentator 2.4 years ago, created a comment with at least 3 up-votes. For C: So what counts as a "novel" classifier?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Scholar 3.0 years ago, created an answer that has been accepted. For A: What is a Gbase?
Scholar 3.0 years ago, created an answer that has been accepted. For A: What is a Gbase?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Resources for flow cytometry bioinformatics
Scholar 3.7 years ago, created an answer that has been accepted. For A: What is a Gbase?
Scholar 3.7 years ago, created an answer that has been accepted. For A: What is a Gbase?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 667 users visited in the last hour