search for: transcriptomics

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

...essing the issue of healthcare-associated infections and biomarker evaluation in case control or cohort studies : multivariate analyses, survival studies, etc ... The candidate will work as part of a multidisciplinary group of several research teams with expertise in Immunology, Molecular Biology, Transcriptomics, Biostatistics and BioInformatics. Required qualifications Highly motivated candidates must hold a Ph.D. or engineer degree with a strong background in bioinformatics and in biostatistics. Strong skills in routine biostatistics and bioinformatics tools (R statistical language, python) are requi...

I am attempting to join several dataframes that summarize sampling effort for different samples into one large data.frame/table. I have looked at the merge command, but have not been clever enough to figure out how to get it to do what I want. A simplified example of what I am trying to do: The dataframes I have look like this (they were generated using the table command) species1.effort

*The Jenner Institute is seeking to appoint an outstanding Bioinformatician to run a Transcriptomics Core Facility at the Jenner Institute and to identify, develop and integrate bioinformatics resources into the research programmes of the institute. You will be based at the Jenner Institute in the Old Road Campus Research Building, Headington, Oxford and working in conjunction with Gilean McVe...

...width / height ratio. Here is a typical example : dev.new() heatmap(matrix(rnorm(1200), nrow=10)) I have a non square matrix to plot with heatmap, as there are many more columns than rows, row labels are larger than necessary but column labels can't be read (this is quite common in transcriptomics, where there are many more genes than samples studied). With a classical plot, this could be fixed using a non square device area : dev.new(width=10, height=5) heatmap(matrix(rnorm(1200), nrow=10)) But as can be seen, heatmap don't make profit of it and leave empty room on each side...

*The Jenner Institute is seeking to appoint an outstanding Bioinformatician to run a Transcriptomics Core Facility at the Jenner Institute and to identify, develop and integrate bioinformatics resources into the research programmes of the institute. You will be based at the Jenner Institute in the Old Road Campus Research Building, Headington, Oxford and working in conjunction with Gilean McVe...

Dear Sir/ma'am, I'm using R-3.4.4 and TCGAbiolinks package for the analysis of GDC data. Till today i have reintalled R and R studio for 5 times but one error comes when i analyze the GDC data at the step GDCprepare. the data i am using is not a legacy data of GDC data portal. I think the problem is with my Laptop only because i have run the same commands in another PC and there was no

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...methodologies: regularized CCA and sparse PLS to unravel relationships between two heterogeneous data sets of size (nxp) and (nxq) where the p and q variables are measured on the same samples or individuals n. These data may come from high throughput technologies, such as omics data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, mixOmics can also be applied to any other large data sets where p+q>>n. rCCA is a regularized version of CCA to deal with the large number of variables. sPLS allows variable selection in a one st...