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Hello All The third virtual conference on genomics and bioinformatics will host by North Dakota State University September 16-19, 2003 More details http://www.ndsu.edu/virtual-genomics/conference_2003.htm Call for papers and 2002 accepted papers http://www.ndsu.edu/virtual-genomics/papers_2003.htm Third Virtual Conference on Genomics and Bioinformatics: September 16-19, 2003 Advances in

Hi,     I want to use segChrom() method in tilingArray package. For that I need to create a probeAnno object. I could not find much much info by ?probeAnno. I need help in creating  probeAnno object. Snap shot of the file(.txt): chr1 2500014 2500038 + 0.232689943122845 chr1 2500039 2500063 + 2.60502410304227 chr1 2500062 2500086 + 0.0756595313279895 chr1 2500080 2500104 + 0.78574617788405 chr1

I'm trying to read some web tables directly into R. These are both genome sequencing projects (eukaryotes and metagenomes) from NCBI and look very similar; however, only the first one works. http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi I added ?dump=selected to the end of the url string to get a tab- delimited file (w...

Genome Institute of Singapore (GIS) Biostatistics Group The Genome Institute of Singapore ( http://www.gis.a-star.edu.sg <http://www.gis.a-star.edu.sg> ) is looking for statisticians who are interested in a wide range of biomedical probems. We are especially interested in hearing from senior r...

Por si es de interés: Data Analysis for Genomics Data Analysis for Genomics will teach students how to harness the wealth of genomics data arising from new technologies, such as microarrays and next generation sequencing, in order to answer biological questions, both for basic cell biology and clinical applications. https://www.edx.org/course/harvardx/harvardx-ph525x-data-analysis-genomics-1401

Hi, is there any package/function in Bioconductor that can do this: if given the chromosome positions of a fragment, find out all genes within, and with the information about which strand is the sense strand. And vice versa. Thanks a lot. ----- Appreciate your time & attention! -- View this message in context: http://www.nabble.com/list-genes-w-n-a-genomic-fragment-tp18331452p18331452.html

Hello, I am using R to look at whole-genome gene expression data. This means about 27,000 genes, each with a vector of numbers reflecting expression at different tissues and times. I need to do an all against all co-expression calculation (basically, just calculate Pearson's r for every gene-gene pair). I try to store the result of such...

I wrote a package which includes a number of genome sequencing project statistics on the web like http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi. I included some generic functions to summarize, plot, and update the tables with the most recent version data(lproks) update(lproks) [1] "lproks successfully updated, 7 new genomes added"...

Hello, I have a data frame (68,000 rows) of scores (V4) for a series of [genomic] coordinates ranges (V2 to V3). I also have a data frame (1.2 million rows) of single [genomic] coordinates. For each genomic coordinate (in coord), I would like to determine the average of all scores whose genomic ranges (in scores) encompass the coordinate (in coord). To accomplish this, I tried: The

Hi everybody, I am trying to make my mind about the use of R for Computational and Statistical Approaches to Genomics. I know this is a vaste field: this is the main reason why I am sending this message to this always useful list! Any key/entry point to this field will be extremely welcome! Please, could you help me to go in the right direction? Thanks!!! Ricardo -- Ricardo Rodr?guez

Hi, > url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" > download.file(url, tempfile()) trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' Error in download.file(url, tempfile()) : cannot open URL 'ftp://ftp.ncbi.nlm.nih.gov/genome...

...loosing strand information was to manually substitute an "R" to "-" and an "F" to "+" in the file before reading it in R. But it is much more cumbersome since the use of + and - is, for example, a standard format in bed files accepted and generated by the Genome Browser and other genome sites. Please let me know what do you think. Ps. I saw this first in the Fedora version (rpm automatically updated), but it is reproduced also in the Windows version. Thank you all people for your work and for making R the wonderful tool it is! Cheers, Margherita --...

Dear all: I installed the rsync 2.5.4 in my two machine (192.168.1.30 and 192.168.1.120, both are AIX OS) to backup data each other. The software`s installation is ok, and I can copy local files. But when I try to backup data between two machines, there reports some errors: >./bin/rsync -avz 192.168.1.30::web ./backup-3000/ rsync: failed to connect to 192.168.1.30: Connection refused

...haelson lab investigates the effect of genetic variation on the development and function of the brain, particularly in the context of neurodevelopmental conditions such as autism and language impairment. Our work revolves mostly around integrating information from large scale data sets (e.g., whole genome sequencing, RNA-seq, ChIP-seq, etc.) and deriving informative features so that predictive models can be built and used to better understand the molecular basis of neurodevelopmental conditions. This postdoctoral position will be devoted mostly to developing models that estimate the downstream effe...

Dear useRs, I am glad to announce that the new R package "hypred", initial version 0.1, is now available on CRAN. "hypred" is a package for simulating high-density SNP data. Its main function, "hypredRecombine" is intended to be used as a "Software tool" in larger programs that simulate complex populations. The focus of the package is on producing

Dear useRs, I am glad to announce that the new R package "hypred", initial version 0.1, is now available on CRAN. "hypred" is a package for simulating high-density SNP data. Its main function, "hypredRecombine" is intended to be used as a "Software tool" in larger programs that simulate complex populations. The focus of the package is on producing

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 c...

Dear all, I''m trying to write a function, that will take as an argument, some aligned genome sequences, and using a sliding window, do pairwise comparisons of sequence similarity. Coding the sliding window I think I can manage but what I''m trying to get to grips with is getting it so as every pairwise comparison is made, no matter how many genomes are added, from 3 to N. So if I...

...search across Manchester (www.mcrc.manchester.ac.uk<http://www.mcrc.manchester.ac.uk/>). The ACBBG incorporates postdoc-level bioinformaticians and computational biologists who provide collaborative support for the analysis of high throughput genomics data, including ChIP seq, RNA seq, whole genome DNA sequencing, microarrays and quantitative protein mass spectrometry. Based within the ACBBG, and part of an interdisciplinary team featuring programmers, computational biologists and bench scientists, senior analysts work collaboratively for extended periods with other research groups within the...

Hi, I noticed some time ago that, for instance, named vectors that are really makes str() really slow when displaying the names attribute. I don't know exactly when this started, but it wasn't the case say 1-2 years ago. Example (on a WinXP 1.8GHz): > s <- 1:1000; names(s) <- s > system.time(str(s)) Named int [1:1000] 1 2 3 4 5 6 7 8 9 10 ... - attr(*, "names")=