User: Adrian

gravatar for Adrian
Adrian680
Reputation:
680
Status:
Trusted
Location:
Cambridge, MA
Website:
http://www.empiricist.ca
Last seen:
11 months ago
Joined:
8 years, 11 months ago
Email:
a*******@gmail.com

Posts by Adrian

<prev • 29 results • page 1 of 3 • next >
1
vote
1
answer
1.2k
views
1
answers
Answer: A: data mining: find expression level of a specific gene in specific tisse
... Are you looking at a particular dataset in GEO?  More specific details would be helpful. You might want to have a look at GTEX, which is a large systematic dataset of gene expression and eQTLs across many human tissues: http://www.gtexportal.org/home/ ...
written 4.6 years ago by Adrian680
0
votes
4
answers
5.0k
views
4
answers
Comment: C: Gene set enrichment tool for RNA-Seq in Python?
... Just set some cutoffs and run hypergeometric tests by computing overlaps using python sets and calculating significance with scipy.stats.hypergeom and statsmodels.sandbox.stats.multicomp  ...
written 4.8 years ago by Adrian680
0
votes
2
answers
1.1k
views
2
answers
Comment: C: Tool for finding unique sets of proteins
... It depends what one wants.  If, as the question states, one wants to find the unique proteins in the set, then the problem is to do exact clustering.  Doing that is going to be very much faster than doing the NxN BLAST.  I agree that if the questions are more subtle, having the NxN BLAST results to ...
written 4.8 years ago by Adrian680
0
votes
1
answer
1.1k
views
1
answers
Comment: C: Tool to map sequences and get genomic coordenates
... Did the pieces originally come from the same region?  If so, but the individual pieces are so short that they align in multiple places, could you use BLAT (or indeed, BLAST) to find all those alignments, and then find the locations where there are clusters of pieces aligning in the same area, and do ...
written 4.8 years ago by Adrian680
1
vote
1
answer
1.1k
views
1
answers
Answer: A: Tool to map sequences and get genomic coordenates
... BLAT: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start ...
written 4.8 years ago by Adrian680
0
votes
2
answers
1.1k
views
2
answers
Answer: A: Tool for finding unique sets of proteins
... BLAST would be doing much more work than is necessary to solve the problem you've posed. The most popular tools for clustering sequences to find the unique ones are probably CD-HIT http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi and USEARCH http://drive5.com/usearch/ ...
written 4.8 years ago by Adrian680
1
vote
3
answers
2.1k
views
3
answers
Answer: A: question about clustering of samples
... You need to drill down and look at your data in more detail (ie. at the level of gene expression), and figure out what exactly about the expression profile is making these things cluster the way that they do.  There's something funny, but you can't tell what it is from just the dendrogram.  It does ...
written 4.8 years ago by Adrian680
3
votes
4
answers
5.0k
views
4
answers
Answer: A: Gene set enrichment tool for RNA-Seq in Python?
... There's nothing about gene set analysis that is dependent on array probe Ids; once you have gene level expression measurements (ie. indexed by gene symbol or entrez gene id) you can use any of the existing tools (eg GSEA).   Some of them do have features to convert from probesets to gene symbols, bu ...
written 4.8 years ago by Adrian680
2
votes
1
answer
1.4k
views
1
answer
tool for quick,exon structure comparison for a gene between two organisms
... Can anyone suggest a tool/server, that given the name of an annotated gene, will quickly make a nice figure summarizing the alignment & conservation of exons and structure of known transcripts between two organisms (ie. mouse vs human)? I could do the alignments and draw it myself, but surely t ...
visualization genomics comparative written 4.8 years ago by Adrian680 • updated 4.8 years ago by Sam2.2k
3
votes
3
answers
3.7k
views
3
answers
Answer: A: Number Of Transcription Factor Binding Sites In The Promoter Of A Gene
... An extra layer of information that is now available and worth considering is DNAse I hypersensitivity and digital footprinting data (which has been generated systematically in a variety of both human and mouse cell types by ENCODE). The idea is that in a particular cell type, regions that are trans ...
written 5.3 years ago by Adrian680

Latest awards to Adrian

Popular Question 17 months ago, created a question with more than 1,000 views. For Human Expression Compendium?
Appreciated 3.8 years ago, created a post with more than 5 votes. For A: How To Efficiently Parse A Huge Fastq File?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Human Expression Compendium?
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Calculating Averages For Windows
Epic Question 3.9 years ago, created a question with more than 10,000 views. For Correlation Between Genome Conservation Scores (Phastcons Vs. Phylop)?
Scholar 4.5 years ago, created an answer that has been accepted. For A: data mining: find expression level of a specific gene in specific tisse
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Where To Get A List Of Species?
Appreciated 5.0 years ago, created a post with more than 5 votes. For A: Should I Do A Dual Master Degree In Both Bioinformatics And Cs?
Appreciated 5.0 years ago, created a post with more than 5 votes. For A: Where To Get A List Of Species?
Appreciated 5.0 years ago, created a post with more than 5 votes. For Correlation Between Genome Conservation Scores (Phastcons Vs. Phylop)?
Great Question 5.0 years ago, created a question with more than 5,000 views. For Correlation Between Genome Conservation Scores (Phastcons Vs. Phylop)?
Good Question 5.0 years ago, asked a question that was upvoted at least 5 times. For Correlation Between Genome Conservation Scores (Phastcons Vs. Phylop)?
Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: Where To Get A List Of Species?
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Correlation Between Genome Conservation Scores (Phastcons Vs. Phylop)?
Supporter 5.0 years ago, voted at least 25 times.
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Should I Do A Dual Master Degree In Both Bioinformatics And Cs?
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Where To Get A List Of Species?
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Macosx For Bioinformatics?
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Calculating Averages For Windows
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How To Find Homology Between Multiple Sequences In Fasta Format?
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How To Efficiently Parse A Huge Fastq File?
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How Do I Match Orthologues In One Species To Another, Genome Scale?
Student 5.0 years ago, asked a question with at least 3 up-votes. For Correlation Between Genome Conservation Scores (Phastcons Vs. Phylop)?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 956 users visited in the last hour