Bioconductor Forum

Tremendous opportunities for discovery are emerging in the biological and biomedical sciences, as well as in traditional physical and social sciences, but they will require the combined power of theory, data analysis, and simulation. In the biomedical sciences, for example, researchers are being confronted by an explosion of information from genome sequencing, gene expression profiling, prote…

Research

updated 4.3 years ago • simonsF.careers

Eurac Research is looking for a __Postdoctoral researcher in Computational Metabolomics__   The Institute for Biomedicine is seeking a highly motivated researcher to join the Computational Metabolomics team.   The Institute for Biomedicine is home to an international and interdisciplinary team of scientists, students and support staff, integrated in an excellent n…

xcms metabolomics population metabolism job Job

updated 7.0 years ago • Johannes Rainer

and evolution of the vertebrate brain and its constituent substructures and cell types. Possible projects involve comparative/bioinformatics analyses of extensive single-cell transcriptomic, epigenomic, and spatial...jawless vertebrates, such as the sea lamprey, to mammals, such as platypus and human. The precise projects will be developed together with the candidate, based on their interest. …

PhD single-cell ComparativeGenomics evolution

updated 4.2 years ago • henrik.kaessmann

the biological processes behind human diseases and provide actionable treatment insights. The project will focus on developing hierarchical modelling and scalable inference approaches that flexibly borrow information...proteomics, metabolomics) and public annotations. The methods will be used in ongoing collaborations with biologists and clinicians, in particular to tackle research questions a…

molecularQTL biostatistics computationalbiology GWAS

updated 3.6 years ago • helene.ruffieux

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updated 19.7 years ago • Justin Zhang

I apologize in advance if this is not a proper forum for this kind of post. We are looking for an individual to help us integrate some of the Bioconductor tools and a few other algorithms into our product. The work would be done in Chiang Mai, Thailand and have an estimated duration of 3-4 months. In addition to being a commercial venture, we expect that this work would result in a publishable…

updated 16.8 years ago • Boris Umylny

Hello Friend, My name is Mrs.faith King I am a dying woman who has decided to donate what I have to charity through you.You may be wondering why I chose you. But someone has to be chosen. I am 59 years old and was diagnosed for cancer about 2 years ago,immediately after the death of my husband who had left me everything he worked for.I have been touched by the lord to donate from what I have inh…

Cancer Cancer

updated 18.4 years ago • faith King

Hello, I'm having issues with downloading a series matrix file in R 4.2.3. > library(GEOquery) > geoMat <- getGEO("GSE51032") I get the following error message. Error in...Hello, I'm having issues with downloading a series matrix file in R 4.2.3. > library(GEOquery) > geoMat <- getGEO("GSE51032") I get the following error message. Error in data.…

getGEOerror

updated 2.8 years ago • suyonj

mean. This would be useful for me because I seem to be continuously runiing fix(), exiting from the editor, running the function, fix() and so on. Thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at

Cancer Cancer

updated 17.7 years ago • Daniel Brewer

GSE22216") but this will fail to get data with error as below. <ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE22nnn/GSE22216/matrix/> Error in function (type, msg, asError = TRUE)  :   Failed to connect to [ftp.ncbi.nlm.nih.gov...it, would you teaching me ? > a6 <- getGEO(filename="[ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE22nnn/GSE22216/matrix/G…

getGEO

updated 9.9 years ago • maedakus

This data.frame is obtained from AnnotationHub and the source is from Epigenomics RoadMap Project. The below is codes help you see the problem. <pre> library("AnnotationHub") ah <- AnnotationHub() epiFiles <- query(ah, "EpigenomeRoadMap

annotationhub roadmap project rpkm data.frame

updated 9.2 years ago • wcstcyx

3.4.4. The Bioconductor Version that has been available for use for this R Program versions on my personal computer and laboratory computer is Bioconductor 3.6. I have been experiencing a problem with using the "getGEO...nbsp;  and then try to use getGEO to upload the microarray expression set (both GDS and GSE Series Matrix/SOFT Family Files), the R Program responds back saying that th…

microarray software error bioconductor affy R

updated 7.8 years ago • drobinson289

<div class="preformatted">So here goes, I am about to risk getting myself blacklisted by the very people I can least afford to be blacklisted by, and at the very start of my career no less. Why am I taking this risk? Because I love Bioconductor, it's the most useful thing currently installed on my PC, and I'm deeply grateful to the developer and user community for making such a wonderful to…

GUI GUI

updated 21.9 years ago • Alex F. Bokov

working in a fast moving industry environment. ## Responsibilities * Opportunity to own a project with guidance from a mentor, collaborate with other scientists, perform data analysis and present the results. * Create

internship genomics genetics Job

updated 6.9 years ago • Steve Lianoglou

candidate will join a team of biostatisticians and bioinformaticians working on a wide variety of collaborative projects in cancer research. The positions will have a primary focus in bioinformatics. Requirements: MS in

Cancer Cancer

updated 18.1 years ago • caiwei@mdanderson.org

as well as integrating proteomic data with genomic and metabolomic data. Our group is highly collaborative, participating in national and international consortia in which teams of scientists, statisticians, and...Bioinformatics/ Computational Biologist to join our proteomics team to help drive translational projects forward towards clinical applications by performing analysis and interpretation o…

SEATTLE WASHINGTON WASHINGTON STATE BIOINFORMATICS COMPUTATIONAL BIOLOGY Job

updated 5.8 years ago • Fred Hutch (Recruiting)

design matrix out out keep it in ? I was also wondering if this is the best approach for time series analysis with no replicate ? In EdgeR manual also mentioned that a reduced model matrix could be used in conjuction

edger

updated 6.2 years ago • sirintra

Hi all, I have a set of RNA-seq data. It's a time series with 4 stages of leaf development, 2 treatments, and 3 bio-reps per stage x treat combo. I've already found DEGs for the...Hi all, I have a set of RNA-seq data. It's a time series with 4 stages of leaf development, 2 treatments, and 3 bio-reps per stage x treat combo. I've already found DEGs for the treatments

deseq2 RNA-seq

updated 6.7 years ago • jamesfischer047

out! Bioinfguru Edits: 1. 19/4/24 - The scope of this tutorial is for those installing on personal machines (sudo privilage is required). Next time I install, I'll be trying to install as guest, without sudo to see what

bioconductor Install

updated 20 months ago • BioinfGuru

a highly dynamic environment, embedded in a team of passionate scientists working on a wide range of projects related to translational stem cell biology. They will have a chance to interact with experienced bioinformaticians...at NCATS and collaborators at top-academic institutions. **Core Responsibilities**: Computational analysis is integral to the lab's efforts...The individual should prom…

JobPosting

updated 4.6 years ago • hannah.baskir

in the Department of Genetics at Stellenbosch University, Stellenbosch, South Africa Project Description: This project is a collaborative effort between the Departments of Genetics and Psychiatry at Stellenbosch...sun.ac.za> by 2 May 2012 1) Letter of motivation stating why the candidate is suitable for this project 2) Curriculum vitae 3) The names and contact details of two refer…

Sequencing Genetics Pharmacogenomics Sequencing Genetics Pharmacogenomics

updated 13.7 years ago • Warnich, Louise <lw@sun.ac.za>

Cancer Genomics lab of Dr. Rendong Yang. The goal of this position will be to lead multiple research projects, develop novel computational algorithm(s), perform data analysis, collaborate with biologists and physicians, and...dimensional genomic data to understand the initiation and progression of diseases. The research projects involve in the development of highly accurate and sensitive computat…

cancer genomics bioinformatics machine learning next-generation sequencing Job

updated 8.6 years ago • yang4414

Biology at the University of Massachusetts Medical School, located in Worcester MA. Research projects in Dr. Zhu's group include (1) development of bioinformatics algorithms and tools for integrative and interactive...Methods __2019__) * NADFinder (Genome Research __2019__) * dagLogo * InPAS This is a collaborative project consisting of a multidisciplinary effort spanning multipl…

single cell sequencing multi-omics data mining and integration Job

updated 6.4 years ago • Julie Zhu

unfortunately all of the samples with inferior RNA-quality (low RNA-content) were measured in the third cartridge. (Fortunately,  the advanced cancer samples are not significantly over/under-represented in the third

deseq2 confounders nanostring rnaseq differential gene expression

updated 7.8 years ago • kim.malek88

to the whole genome sequence data of 40,000 cancer genomes from Genomics England’s 100,000 Genome project. Genomics England’s 100,000 Genome project is a large-scale initiative, backed by the UK government, to sequence samples

phd cancer pathogens NGS Job

updated 8.7 years ago • Daniel Brewer

pre> gse=getGEO("GSE106977",GSEMatrix=T) #<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106977/matrix/">https://ftp.ncbi.nlm.nih.gov/geo/series/GSE106nnn/GSE106977/matrix/</a> #OK #Found 2 file...s) #/geo/series/GSE106nnn/GSE106977/ #Error in download.file(sprintf("<a href='https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",&a…

R GEO geoquery geoquery error message Tutorial

updated 8.0 years ago • martinguerrerog89

Your email client cannot read this email. To view it online, please go here: http://www.absolutebase.com/email/display.php?M=65187&C=ee50eb511786aa dd9385c5491b2591ca&S=36&L=170&N=11 To stop receiving these emails:http://www.absolutebase.com/email/unsubscribe.php?M=65187&C=ee5 0eb511786aadd9385c5491b2591ca&L=170&N=36 [[alternative HTML version deleted]]

GO GO

updated 16.7 years ago • ABSOLUTE PROJECT

statistical and computational methods for processing and interpreting genome-scale datasets in close collaboration with biologists, spanning basic and clinical applications. For further information, see <http: mrobin="" tiny.cc...from high-throughput genomic technologies (e.g. massively parallel sequencing). Several exciting projects are now underway, including but not limited to methods for…

ASSET ASSET

updated 14.2 years ago • Mark Robinson

candidate will join a team of biostatisticians and bioinformaticians working on a wide variety of collaborative projects in cancer research. The positions will have a primary focus in bioinformatics. Minimum Requirements

Proteomics Cancer Proteomics Cancer

updated 17.7 years ago • caiwei@mdanderson.org

Hello everyone! I'm new in RNAseq data analysis and trying to apply a pipeline from an online course to A.thaliana data in my university course project. The pipeline includes kallisto quantification with subsequent analysis in R. I performed kallisto quantification with A.thaliana transcriptome, which I downloaded from plants.ensembl.org, got all the esential files. Firstly, I imported studydesi…

tx2gene tximport Arabidopsis_thaliana kallisto

updated 3.1 years ago • Mikhail Biryukov

and metastasis. Prospective postdocs will have the opportunity to work on one or more funded projects and collaborate with multiple groups at national and international research centers. **Key Responsibilities (include...optimization of advanced computational biology methods for the integrative analysis of genomics data. - Collaborate with molecular and cell biologists to investigate the mol…

SingleCell Transcriptomics SpatialDatasets SpatialData

updated 19 months ago • Silvio

unit of the German centre for infection research (<a href="http://www.dzif.de/">www.dzif.de</a>) and collaborates locally, nationally and internationally with biologists and medical experts from universities and research...to study the evolution of influenza viruses from genomic and phenotypic data sets.  Related projects, as well as newly established collaborations, offer pl…

job bioinformatics computational biology post-doc postdoc Job

updated 9.2 years ago • cristina della beffa

bioinformatics support and training to end-users (research laboratory staff, remotely located collaborative users); 5. Responsible for researching, planning, implementing, and testing bioinformatics software tools...that meet the analysis needs for specific collaborative projects; 6. Development and support of tools and protocols for data deposition to external repositories

cancer bioinformatics bioinformatician job sequencing Job

updated 7.4 years ago • gabriel.wajnberg

GSEMatrix = TRUE) but I receive the following error https://ftp.ncbi.nlm.nih.gov/geo/series/GSE6nnn/GSE6929/matrix/ OK Found 2 file(s) /geo/series/GSE6nnn/GSE6929/ Error in file(con, "r") : cannot open the connection In...addition: Warning messages: 1: In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : URL https:…

r geo getgeo

updated 7.5 years ago • jaleh.amo

for the design and execution of cutting-edge data analysis workflows for the experimental projects in the group. The position is situated in the group of Matthias Hentze at the EMBL in Heidelberg, Germany, with a joint...appointment with the group of Wolfgang Huber in the Genome Biology Unit. Medically-relevant RBP projects emerge from collaborations within the Molecular Medicine Partnership Uni…

Sequencing Sequencing

updated 13.7 years ago • Wolfgang Huber

gt; gset<-getGEO("GSE59856",GSEMatrix=T,destdir="f:/") https://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59856/matrix/ OK Found 2 file(s) /geo/series/GSE59nnn/GSE59856/ Error in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov...geo/series/%s/%s/matrix/%s",  :    cannot open destfile 'f:///geo/series/GSE59nnn/GSE59856', reason 'No such file…

bioconductor

updated 8.0 years ago • comeherewinter

Hi, This is a follow question related to https://support.bioconductor.org/p/89021/. I have a list of barcodes and would like to get all the metadata possible for them in a flat table (or maybe a DataFrame with some list columns) from TCGA. The issue is that the \_indexed\_ data available from TCGA is incomplete so downloading a json file via the GDC api or with \`TCGA::GDCquery\_clinic…

tcgabiolinks

updated 9.2 years ago • Leonardo Collado Torres

Identify and lead efforts to apply for and solicit internal and external funding opportunities, in collaboration with PIs to update and/or expand the Metabolomics facility technologies. • Respond to requests from PIs to...concepts for new projects and provide consultation on technical and scientific aspects of research projects, protocols, and grant proposals...letters of support and technical d…

Metabolomics

updated 3.8 years ago • Jenny Drnevich

__CALL FOR PAPERS__ __International Journal of Approximate Reasoning__ __Special issue on Statistical and Computational methods for genomics and integrative genomics__ __ __<http://www.journals.elsevier.com/international-journal-of-approximate-reasoning/call-for-papers/special-issue-on-statistical-and-computational-methods-for-g/>   __Background and Scope:__ In the l…

news call News

updated 10.4 years ago • rancoita.paola

Sandmann, eLife, 2015](http://elifesciences.org/content/early/2015/03/06/eLife.05464) ). In this project, you will develop new statistical methods for high-dimensional screening data and genetic interaction data. The...project requires the development of thorough statistical methods to analyze high-throughput imaging data as well as network...The candidate should have interest in molecular or med…

high-throughput screening interactions genetics jobs image analysis Job

updated 10.7 years ago • Bernd Fischer

the understanding of lung diseases at the genomic level using the microarray technology. Our current collaborative projects include disease class prediction in sarcoidosis, biomarker identification in lung cancer, gene...of normalisation, effects removing, sample classification and disease class prediction. This project should lead to the creation of statistical package including a set of methods…

Microarray Classification Cancer Lung Microarray Classification Cancer Lung

updated 19.8 years ago • Florent Baty

a rare opportunity to run R in a system with 64GB memory without any limit on memory usage for any person or process. However, I encountered the memory problem error message like this: Error: cannot allocate vector of size...when the length of a vector is larger than 2^31-1. I wonder the problem has anything to do with the third case. (If so, then I think I am hopeless unless the internal implem…

PROcess trigger PROcess trigger

updated 21.0 years ago • Tae-Hoon Chung

My data set contains three factors i would like to analyze in a time-series using the DESeq2 package I have stimulated vs. unstimulated cells i have knockout vs. wildtype i have three time-points

time-series DESeq2

updated 4 months ago • gogeni5529

Maybe this is not the conventional way, but allows me to update all libraries without creating a new personal folder each time R is updated to a new version. Hope this help, Andrea ----- Messaggio inoltrato da stvjc at channing.harvard.edu...you? If it does not, you should study the R installation and administration guide available at R project manuals, and pose residual questions at r-help. D…

safe safe

updated 14.1 years ago • Andrea Grilli

NA, Colv = NA) Presumably, the first row should be all black because all entries are "1", and the third row should be all white cause all entries are "0". But the heatmap shows both the first and third rows are white. When I use

updated 20.9 years ago • Dongxiao Zhu

building libraries. - it would be nice to have some place where one can see what sorts of projects are being done so that collaboration etc can go on. - perhaps a Wiki type interface? thanks robert -- +--------------------------------------------------------------------- ------+ | Robert Gentleman

GO GO

updated 24.1 years ago • rgentleman

at the IFOM- IEO Campus in Milan. The candidates will have the opportunity to work on cutting edge projects in cancer development and evolution. They will become familiar with gene expression and regulation, epigenetics...and medical organizations in the area. The European School of Molecular Medicine (SEMM) in collaboration with the Italian Institute of Technology (IIT) in Genoa coordinates the …

Sequencing Epigenetics Cancer Sequencing Epigenetics Cancer

updated 14.4 years ago • mattia pelizzola

Provide bioinformatics and biostatistics support to colleagues within Monogram and external collaborators. ? Manage bioinformatics projects. ? Perform strategic planning for bioinformatics analysis tools and methods

updated 12.9 years ago • Agnès Paquet

for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages

rtracklayer

updated 4.7 years ago • nick.shrine

for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages...for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' …

cdf Biobase affy cdf Biobase affy

updated 19.8 years ago • Jenny Drnevich

<div class="preformatted">In working through the example in the documentation 'Text Description of affy' I receive the following errors with regard to loading the example data: > data(listcel) Error: restore file may be from a newer version of R -- no data loaded > data(CDF.example) Error: restore file may be from a newer version of R -- no data loaded > I can generat…

cdf cdf

updated 23.5 years ago • Carleton Garrett

__Job Description__ We are seeking a __highly motivated junior-level postdoctoral researcher__ to join the Voice Research Laboratory, Faculty of Medicine at McGill University in Canada. This appointment is expected to begin in September 2018 (start date negotiable). It is a 3-year position with possibility of extension. The Voice Research Laboratory focuses on advancing&nb…

abm postdoc computational biology personalized medicine biomedical science Job

updated 7.7 years ago • nicole.ykli

for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages...interface to help. Type 'q()' to quit R. > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE) …

AnnotationHub

updated 7.7 years ago • Robert K. Bradley

http://32xiang.appspot.com/2009/10/7/r_stat_bookmarks_999.html 1 http://www.r-project.org/ "The R Project for Statistical Computing" 2 http://addictedtor.free.fr/graphiques/ "R Graph Gallery" 3 http://zoonek2.free.fr/UNIX...6 http://wiki.r-project.org/rwiki/doku.php "wiki for R" 7 http://www.rseek.org/ "RSeek.org R-project Search Engine" 8 http://had.co.nz/ggplot2/ "GGPLOT" 9 http://pj.freefacul…

Sequencing Microarray Genetics Visualization Network Bayesian Classification Clustering

updated 15.6 years ago • David Lyon

<div class="preformatted">Post-doc, Statistical Genetics Murdoch Childrens Research Institute For further information about the position please contact Dr Stephen Leslie (email: stephen.leslie at mcri.edu.au or telephone: +61 3 9345 7042). Please note that excellent candidates with a strong statistical background from any quantitative scientific discipline (e.g. physics, engineering, ...)…

Genetics Genetics

updated 12.7 years ago • Lavinia Gordon

servers/servlet containers (jBoss, Tomcat, GlassFish/Sun Application Server) is advantageous. This project is funded by the BBSRC and forms part of the collaboration of Alvis Brazma's and Wolfgang Huber's groups at the EBI. If...you have questions, you may contact the project coordinator Misha Kapushesky (ostolop at ebi ac uk). Contract: An initial 1 year contract will be offered to the success…

Microarray GUI ArrayExpress Microarray GUI ArrayExpress

updated 19.4 years ago • Misha Kapushesky

Hi, I'm trying to use DESeq2 to perform time series analysis like a one-way ANOVA on multi-groups of samples,but there is a obvious batch effect in my data . I would like to

deseq2 time series remove batch effect

updated 6.9 years ago • Nicola

Hi everyone! I have a question that I would really appreciate it if you help me out, please! I have a list of data that I would like to know how to find out the gene's names in the regions. The dataset which is a text file has the following format: Segment Count First End 0 258 1_1960674 1_…

annotation

updated 6.7 years ago • ari_sh70

Hello, I need guidance about a time series experiment in which two treatment groups share a common time 0 control. The purpose is to evaluate the effects of hypoxia

timeseries

updated 3.0 years ago • Brynn

Good English language skills - Work permit for the European Union __We offer:__ - Exciting projects and a stimulating working environment - Ongoing academic qualification in the field of Bioinformatics and Statistics...opportunity employer. Universitätsmedizin der Johannes Gutenberg-Universität Mainz Servicecenter Personal und Recht – Recruiting Büro Langenbeckstraße 1 55131 Main…

bioinformatician job rnaseq statistics systemsbiology Job

updated 10.7 years ago • Federico Marini