User: Marcin Cieslik

gravatar for Marcin Cieslik
Reputation:
520
Status:
New User
Location:
Last seen:
7 years, 1 month ago
Joined:
9 years, 2 months ago
Email:
m****@virginia.edu

Posts by Marcin Cieslik

<prev • 35 results • page 1 of 4 • next >
0
votes
3
answers
7.3k
views
3
answers
Comment: C: How To Read A Bigwig File Using Python
... Just to be sure you are saying that random-access of a BigWig in bx-python is considerably slower than Perl? Maybe profile the python code and see were the time goes. ...
written 7.2 years ago by Marcin Cieslik520
2
votes
1
answer
1.8k
views
1
answers
Answer: A: Identifying Interaction Between Tfs As Regulators Or/And Targets
... We are mapping putative enhancer regions based on multipe epigenetic chip-seq signals. We find that the great majority 95%+ of putative enhancers is within 1Mb of the closest gene, 99% are withing 5Mb. The initial slope is pretty steep with 80% within the 100kb. Regarding TFs binding in promoter reg ...
written 7.3 years ago by Marcin Cieslik520
0
votes
3
answers
1.9k
views
3
answers
Comment: C: Non-Unique Refseq Ids ?
... it is useful that UCSC provides a N:1 mapping to entrez gene ids ...
written 7.6 years ago by Marcin Cieslik520
0
votes
2
answers
4.3k
views
2
answers
Answer: A: Rna-Seq Normalization
... I like the normalization as done in DESeq (http://www-huber.embl.de/users/anders/DESeq/) e.g. translated into python: import numpy as np def size_factors(counts): counts = counts[np.alltrue(counts, axis=1)] logcounts = np.log(counts) loggeommeans = np.mean(logcounts, axis=1).reshape(len( ...
written 7.9 years ago by Marcin Cieslik520
1
vote
3
answers
2.8k
views
3
answers
Answer: A: Probability Of Expression Changes 2-, 5-, ...100-Fold
... (I write from memory as I do not have access to the paper, so this might not be accurate) Having two read counts X and Y for a transcript and the total number of sequenced reads (A and B) the the poisson margin test (introduced here http://www.ncbi.nlm.nih.gov/pubmed/21385042) gives the probability ...
written 7.9 years ago by Marcin Cieslik520
1
vote
3
answers
3.2k
views
3
answers
Comment: C: Java Parser For Bigwig ?
... Excellent example for diving into JNI! ...
written 8.0 years ago by Marcin Cieslik520
0
votes
8
answers
13k
views
8
answers
Comment: C: How To Convert Xml Into A Decent Parseable Format?
... David, would you follow a western-protocol that takes longer if it gives the same end-result? If a tab-file covers 80% of the possible use cases of a data-base it might cover 99% of the real users. I would argue that any database should be available as SQL or RDF/XML AND TAB to be accessible to as m ...
written 8.0 years ago by Marcin Cieslik520
3
votes
5
answers
4.2k
views
5
answers
Answer: A: Library / Module For Network Analysis
... I would suggest [Gremlin](http://github.com/tinkerpop/gremlin/wiki/). It is a domain specific language (DSL) to analyze (think algorithms) and explore (think traverse) graphs originally influenced by XPath. The implementation is superb and the community vibrant. Gremlin sits on top of Blueprints whi ...
written 8.3 years ago by Marcin Cieslik520 • updated 8 months ago by RamRS21k
0
votes
26
answers
36k
views
26
answers
Comment: C: Recommend Your Favorite Bioinformatics Books
... I've not seen this, thanks! ...
written 8.5 years ago by Marcin Cieslik520
4
votes
26
answers
36k
views
26
answers
Comment: C: Recommend Your Favorite Bioinformatics Books
... I a gree a book about technical aspects of bioinformatics, should exist, maybe even in two flavors, "applied data management" and "getting at the bioinformatics data you want", but would you call a statistician someone who happens to know how to write input files to libSVM without knowing what is go ...
written 8.5 years ago by Marcin Cieslik520

Latest awards to Marcin Cieslik

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1020 users visited in the last hour