User: Habil Zare

gravatar for Habil Zare
Habil Zare170
Reputation:
170
Status:
Trusted
Location:
United States/Austin Area
Website:
http://oncinfo.org/
Scholar ID:
Google Scholar Page
Last seen:
7 months ago
Joined:
4 years, 4 months ago
Email:
z***@u.washington.edu

I am an Adjunct Assistant Professor in the Department of Cell Systems & Anatomy at the University of Texas Health Science Center - San Antonio. I am the Principal Investigator of Oncinfo Lab.

I am a bioinformatician and computational biologist, and my primary interest is focused on developing new machine learning algorithms for analyzing complicated, large size, and rich biological data. I have experience with analyzing data provided by a wide range technologies including, next generation sequencing, ChiP-seq, and flow cytometry. I am interested in combining techniques from a variety of fields such as spectral graph theory, feature extraction, Bayesian statistics, Dynamic Bayesian Networks, and deep learning to develop novel algorithms, which can recognize the patterns in the biological or clinical data missed by state-of-the-art methodologies. I am very eager in interdisciplinary collaborations with smart biologists and clinicians to define and accomplish scientific projects with the goal of making discoveries in areas such as molecular and cell biology, cancer diagnosis and prognosis, phylogenetics, genomics, and epigenomics.

Posts by Habil Zare

<prev • 18 results • page 2 of 2 • next >
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Answer: A: An alternative to estimateCellCounts function
... I could not find a "safe" solution using minfi. An "unsafe" solution is using the minfi:::projectCellType (not exported) function as illustrated here.  ...
written 2.9 years ago by Habil Zare170
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Comment: C: Clomial parallel jobs
... You're welcome! ...
written 3.0 years ago by Habil Zare170
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Answer: A: Clomial parallel jobs
... rsub() is an internal Clomial function. You got this error because the qsub command in your cluster does not have -l mem_free= option. Options can vary cluster to cluster.  You can check with your IT support teams and let me know what options are available, and which are required, to submit a job o ...
written 3.0 years ago by Habil Zare170
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Answer: A: Clomial parallel jobs
... It is possible to run Clomial in parallel.  Basically, the idea is to run thousands of jobs on the cluster using qsub. Clomial submits each job by calling the rsub() function, which needs a template similar to this one but everything else is done automatically. Clomial just needs a proper template a ...
written 3.0 years ago by Habil Zare170
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An alternative to estimateCellCounts function
... My question is similar to https://support.bioconductor.org/p/80439/, which was not answered after 6 months. I have beta values from a level 3 TCGA dataset. They are stored in a matrix, where each row corresponds to a locus and each column is a sample. I tried to use the estimateCellCounts() to infe ...
minfi written 3.0 years ago by Habil Zare170
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Answer: A: SamSPECTRAL cluster numbers bug
... Thanks for reporting the bug in SamSPECTRAL _1.23.2 and earlier. It is fixed in version 1.23.4. The new version should be available from devel page in 2 days. I also added an option doOrderLabels. When it is set to TRUE (the default),  "after connecting components, relabeling will be done such that ...
written 4.3 years ago by Habil Zare170
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Answer: A: Test question on SamSPECTRAL package
... Yes, I got the email. ...
written 4.3 years ago by Habil Zare170
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Test question on SamSPECTRAL package
... This is a test post to see if the maintainer get an email notification right. Habil.  ...
samspectral written 4.3 years ago by Habil Zare170

Latest awards to Habil Zare

Scholar 16 months ago, created an answer that has been accepted. For A: 'L-BFGS-B needs finite values of 'fn''-error when running Clomial package
Scholar 16 months ago, created an answer that has been accepted. For A: Pigengene : BN network using consensus module
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Pigengene : BN network using consensus module
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Pigengene : BN network using consensus module
Scholar 2.9 years ago, created an answer that has been accepted. For A: 'L-BFGS-B needs finite values of 'fn''-error when running Clomial package
Autobiographer 4.4 years ago, has more than 80 characters in the information field of the user's profile.

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