User: Nathan Salomonis

Reputation:
70
Status:
Trusted
Location:
Cincinnati Children's Hospital Medical Center
Website:
https://www.cincinnati...
Last seen:
1 month, 3 weeks ago
Joined:
9 years, 7 months ago
Email:
n*********@gmail.com

I am an Assistant Professor at the University of Cincinnati and Cincinnati Children's Hospital in the Division of Biomedical Research.

Posts by Nathan Salomonis

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Workflow/pipeline for detecting isoforms/alternative splicing
... Try AltAnalyze which has a GUI and hence, dependencies are less of an issue (good to still install R and hopach in R). http://www.altanalyze.org The software can be run by GUI or command-line, enables direct analysis of FASTQ files (modification of Kallisto for pseudo-alignment) to derive BAM file ...
written 7 weeks ago by Nathan Salomonis70
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Answer: A: Event-based software for alternative splicing with three conditions?
... The software AltAnalyze meets these different objectives, depending on the type of multi-group test you want to apply. Firstly, it can perform splicing analyses (and gene expression) directly from FASTQ or aligned BAM files (make sure you are using the correct AltAnalyze genome database version). BA ...
written 8 months ago by Nathan Salomonis70
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Answer: A: Altanalyze output question
... Great question with three separate answers: 1) Yes, when performing ICGS (unsupervised subtype discovery), ICGS performs gene set enrichment per guide-gene associated cluster using the BioMarker database of assembled marker genes from 300 tissues and cell types. The current database was derived fro ...
written 2.3 years ago by Nathan Salomonis70
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Answer: A: Alt Analyze: problem with calls of events
... Hi Lalla, If you haven't checked it out already, you can find extensive background information on the algorithms used for alternative splicing detection and interpretation in AltAnalyze here: http://altanalyze.readthedocs.io/en/latest/Algorithms/ http://altanalyze.readthedocs.io/en/latest/ProteinDi ...
written 3.1 years ago by Nathan Salomonis70
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Comment: C: Reliability of Microarray data analysis through "Altanalyze" tool.
... AltAnalyze will produce a set of files in the folder GO-Elite under the folders upregulated, downregulated and regulated with pathway and ontology enrichment analyses that indicate likely regulated biologically relevant terms. The pruned results file will indicate these results and associated genes. ...
written 3.8 years ago by Nathan Salomonis70
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Answer: A: Pseudogenes On Affymetrix Human Exon 1.0St
... AltAnalyze will return expression values for all Ensembl genes linked to exon array probesets. Affy is quite liberal in assigning probesets to any putative expressed regions in the genome. I would make sure that the expression of house keeping genes look to be highly expressed or even include other ...
written 9.6 years ago by Nathan Salomonis70

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