User: Habil Zare

gravatar for Habil Zare
Habil Zare60
Reputation:
60
Status:
Trusted
Location:
United States/Austin Area/Texas State University
Website:
http://oncinfo.org/
Scholar ID:
Google Scholar Page
Last seen:
5 days, 2 hours ago
Joined:
2 years, 6 months ago
Email:
z***@txstate.edu

I am an assistant professor in the Department of Computer Science at Texas State University, and an adjunct assistant professor in the Department of Cellular and Structural Biology 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 • 12 results • page 1 of 2 • next >
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Comment: C: 'L-BFGS-B needs finite values of 'fn''-error when running Clomial package
... You're welcome! I am interested in Clomial performance if you will have a way to assess it. ...
written 5 days ago by Habil Zare60
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Answer: A: 'L-BFGS-B needs finite values of 'fn''-error when running Clomial package
... 1- Two samples are not enough to infer the clonal composition. 2- There are 4 samples in the data you sent me by email. The mutation ratios seem to be very low (~0.01). plot(rowSums(Dc), rowSums(Dt),xlim=c(0,1000), ylim=c(0,30))    Your data has 169 mutations, and with only 4 samples, it's not ...
written 5 days ago by Habil Zare60
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Importing Infinium data files using RnBeads::rnb.execute.import()
... I cannot import beta values using the rnb.execute.import function from the RnBeads package: rnb.execute.import(data.source=c("annotation"=clinicalFile,"beta"=dnamCsvFile), data.type="infinium.data.files",verbose=TRUE) 2016-12-06 10:49:24 3.2 STATUS STA ...
rnbeads written 12 months ago by Habil Zare60
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Answer: A: Minfi: estimateCellCounts rgSet
... See this. ...
written 12 months ago by Habil Zare60
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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 12 months ago by Habil Zare60
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Comment: C: Clomial parallel jobs
... You're welcome! ...
written 14 months ago by Habil Zare60
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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 14 months ago by Habil Zare60
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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 14 months ago by Habil Zare60
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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 14 months ago by Habil Zare60
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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 2.5 years ago by Habil Zare60

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