search for: transcriptome

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 correc...

Job Title : Postdoctoral Position in Biostatistics/Bioinformatics Background The joint research unit between bioM?rieux, international leader in in vitro diagnostic, and Hospices Civils de Lyon, second-largest University Hospital Network in France, develops a research program dedicated to the study of injury induced immunosuppression. This program aims at (i) describing and understanding the

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

Hi R users, I'm a quite extensive user of the heatmap() function, and as many others i'm frequently frustrated by its fixed square 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

*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

...is not available. So i had contaced the Biomart people but they said that the Biomart is working fine. below is the complete R code i am usign with the corresponding error, library(TCGAbiolinks) query.exp <- GDCquery(project = "TCGA-LUAD", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", workflow.type = "HTSeq - Counts", experimental.strategy = "RNA-Seq") query_load <- GDCdownload(query.exp) luad.exp <- GDCprepare(que...

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CRAN (and crantastic) updates this week New packages ------------ * apcluster (1.0.1) Ulrich Bodenhofer http://crantastic.org/packages/apcluster The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are analogous to the Matlab code published by Frey and Dueck. * BioPhysConnectoR (1.6-1) Franziska Hoffgaard