User: Russh

gravatar for Russh
Russh1.2k
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Location:
U. Liverpool
Website:
http://www.liverpoollu...
Last seen:
7 years, 4 months ago
Joined:
8 years, 10 months ago
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r***********@liv.ac.uk

transport physiologist turned network analyst turned sequence analyst http://twitter.com/#!/dubiousGeek

Posts by Russh

<prev • 108 results • page 1 of 11 • next >
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Comment: C: Machine Learning To Find The More Informative Features To Predict And Outcome
... As an aside, scikit in python has a surprisingly good tutorial for this kind of thing: http://scikit-learn.org/stable/index.html ...
written 7.4 years ago by Russh1.2k
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Comment: C: Visualisation Of Interaction
... Try the layout section (force-directed's a good start), try the vizmapper (for changing node/edge visual properties). Ultimately you can either read the manual or play around with cytoscape. I won't be replying to any further subjective visualisation questions, sorry ...
written 7.5 years ago by Russh1.2k
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Answer: A: Visualisation Of Interaction
... Just use Cytoscape's table import function: File -> Import -> Network from table; it's described in depth in the Csc manual (Creating networks: Import Fixed-Format Network Files). You might need to play with the advanced options to ensure that it doesn't split on all whitespace. This will g ...
written 7.5 years ago by Russh1.2k
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'Official' Cell Line Identifiers
... Hi - quick question is there a set of 'official' cell-line identifiers (akin to HGNC/EntrezGene gene symbols etc). I say 'official', because I appreciate there may be more than one attempt at fixing cell line names. All the best Russ ...
written 7.5 years ago by Russh1.2k • updated 8 months ago by Amos Bairoch30
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Answer: A: Enrichment Analysis Without Differentially Expressed Protein List
... Are you studying a single cancer cell line versus a single 'normal'; or do you have multiple lists? There's no reason why you can't do the enrichment analysis, on a single list (you will need to define a background list against which to compare). However, I suspect the enrhiments will be skewed by ...
written 7.6 years ago by Russh1.2k
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Comment: C: Recalculation Of Base Qualities After Realignment
... thanks, however, it is base quality rather than read quality that I'm keen to calculate. I'm sure similar concerns apply ...
written 7.6 years ago by Russh1.2k
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Recalculation Of Base Qualities After Realignment
... hi apologies if this is a trivial question. I've mapped SOLiD reads using BFAST and subsequently realigned the same with SRMA. There is considerably fewer one-off mismatch errors in the SRMA modified data (in fact SRMA looks a superior tool to GATKs local realigner, which I was previously using). ...
written 7.6 years ago by Russh1.2k • updated 7.6 years ago by Arun2.3k
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Comment: C: Why Do Transcription Factors Bind To Intronic Regions Downstream Of The Transcri
... My favourite gene had a bit of that: http://www.ncbi.nlm.nih.gov/pubmed/14623874 Maybe it makes sense for some TFs to be displaced by RNAPol ...
written 7.6 years ago by Russh1.2k
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Comment: C: Why Gene Regulatory Network Is Sparse?
... What was the theory underlying the theoretical results? ...
written 7.6 years ago by Russh1.2k
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Answer: A: What Does A "*" (Star) Mean In Mpileup'S "Read Bases" Column (The 5Th Column)?
... It's the shadow of a deletion. Suppose you have the following as refereence ACGTCGCTCGCTCG and the following is your sequence of interest, relative to the reference ACGAC--TGGCTCG Let's say you received the read ACGACTGG from some sequencing data. This read overlaps the deletion in your sequenc ...
written 7.6 years ago by Russh1.2k

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Autobiographer 7.3 years ago, has more than 80 characters in the information field of the user's profile.
Guru 7.3 years ago, received more than 100 upvotes.
Centurion 7.3 years ago, created 100 posts.
Supporter 7.3 years ago, voted at least 25 times.
Student 7.6 years ago, asked a question with at least 3 up-votes. For Recalculation Of Base Qualities After Realignment
Commentator 8.2 years ago, created a comment with at least 3 up-votes. For C: What Would You Recommend Me For A One Year Project: Develop A Bioinformatics Sof
Commentator 8.3 years ago, created a comment with at least 3 up-votes. For C: What Are The Obsolete Research Topics In Bioinformatics?
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: How To Use Cytoscape To Do Gene Ontology Enrichment Analysis?
Student 8.4 years ago, asked a question with at least 3 up-votes. For Minimal Req'D Info For A Pathway Analysis Experiment
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Good Question 8.4 years ago, asked a question that was upvoted at least 5 times. For Minimal Req'D Info For A Pathway Analysis Experiment
Teacher 8.5 years ago, created an answer with at least 3 up-votes. For A: Learning About Cancer From The Ground Up...
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Good Answer 8.6 years ago, created an answer that was upvoted at least 5 times. For A: Visualizing (Your Own) Protein-Protein (Or Gene-Gene) Interactions

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