search for: silico

Hi All I am wondering if people based on their experience could share what methods one could use to compare two gff/gtf files. The reason why I want to do so is that we have constructed a RNA-Seq based transcriptome and would like to compare it with reference transcriptome we had from in-silico approaches. Ideally we are looking to find out 1. new genes we see 2. transcripts where the start/end side is changed (upstream/downstream) 3. possible gene fusions may be because in-silico approaches were not correct I know some of these could be resolved with BedTools but just wondering if Bio...

...quot;) from within R 3) Since I don't have LATEX for windows, I used texi2dvi from the CYGWIN package 4) When I run the command in Cygwin 'texi2dvi -c -p GeneSpring.tex' I get the error shown below. 5) When I edit the GeneSpring.tex file and comment out the line \usepackage{C:/PROGRA~1/SILICO~1/GENESP~1/data/rw1081/share/texmf/Sweave} and try to convert to PDF again, it will successfully convert the TEX file to PDF. It seems that the Sweave library causes some problems in the parsing of the TEX file. Is there something I forgot to do? Thanks, Thon ------------- OUTPUT FROM texi2dv...

...hell scripting are desirable. Must be thorough, committed to completion and willing to rapidly learn tools as needed. B. Bayesian modeling tools with Stan: Create re-usable tools for the Bayesian modeling of pharmacometrics data that can integrate diverse data sources (including pre-clinical, in-silico model predictions, etc.). Using the latest Stan?s facilities (http://mc-stan.org) develop templates/functions for compartmental PK models and indirect response PK/PD models. Produce documentation in the form of a modeling report and a presentation. Requirements: Second or third year PhD student...

...lopment of statistical methodology, development of software, and co-authorship of publications and presentations are also primary responsibilities. The scope of the nonclinical statistics group focuses on needs outside traditional clinical trials. This includes preclinical in-vivo, in-vitro, and in-silico studies, as well as product formulations. We also serve experimental medicine needs in clinical pharmacology. A Ph.D. or Masters in statistics or appropriate data-analytic discipline is required. The target candidate is one with approximately 5 years of experience as a statistician, but there is f...

...e area northwest of Philadelphia, Pennsylvania, in the USA. Extraordinary applicants from outside the US are welcome, subject to visa limitations. The scope of the nonclinical statistics group focuses on needs outside traditional clinical trials. This includes preclinical in-vivo, in-vitro, and in-silico studies, as well as product formulations. We also serve experimental medicine needs in clinical pharmacology. A Ph.D. or Masters in statistics or appropriate data-analytic discipline is required. Comprehensive understanding of linear models is essential. There are unlimited opportunities to succes...

Is there a package, or does anyone have code they are willing to share, that would allow me to simulate sampling of dead wood pieces across an area? I am specifically looking for code to simulate the dead wood distribution as small line segments across an extent, and then I will "sample" the dead wood using different sampling techniques including line transects, fixed area plots, etc.