Bioconductor Forum

stressors accelerate aging and the development of associated diseases. In this [DFG-funded research project][1] you will investigate (epi-)genomic differences causing mole-rats living several times as long as most other rodents...and self-organization **Our offerings:** - Challenging and varied tasks with a high degree of personal responsibility - Support from and cooperation with competent co…

Epigenomics NGS Aging Biobase

updated 18 months ago • arne.sahm

CCD) at the Massachusetts General Hospital Cancer Center and Harvard Medical School. The CCD collaborates with laboratories in the Cancer Center of the Massachusetts General Hospital to take high-throughput approaches...questions in cancer biology and medicine. This position will focus (at least initially) on projects studying circulating tumor cells. Responsibilities will include: · Wo…

Sequencing Microarray Cancer Sequencing Microarray Cancer

updated 12.0 years ago • Wittner, Ben

CCD) at the Massachusetts General Hospital Cancer Center and Harvard Medical School. The CCD collaborates with laboratories in the Cancer Center of the Massachusetts General Hospital to take high-throughput approaches...questions in cancer biology and medicine. This position will focus (at least initially) on projects studying circulating tumor cells. Responsibilities will include: ? Worki…

Sequencing Microarray Cancer Sequencing Microarray Cancer

updated 12.5 years ago • Wittner, Ben

Hi, I want to perform differential expression analysis of a GSE Series **GSE138214** (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138214) using limma in R. I am unable to extract data...from this series as this series has around 14 different platforms. Using GEOquery and limma package, I am able to differentially analyse...genes in Series **GSE138260** (https://www.ncbi.nlm.nih.gov/geo…

AgilentChip GEOquery limma

updated 3.7 years ago • Prateek

Wed, 1 Oct 2003 11:50:17 -0400 > From: Mike Schaffer <mschaff@bu.edu> > Subject: [BioC] Time series data > To: bioconductor@stat.math.ethz.ch > Message-ID: <f4670cc1-f426-11d7-87bc-000393677ad6@bu.edu> > Content...text/plain; charset=US-ASCII; format=flowed > > Is there a package capable of visualizing time series data a la Gene &gt…

convert convert

updated 22.3 years ago • Nicholas Lewin-Koh

Research Center (DKFZ), where you will join a capable and dedicated team of statisticians engaged in collaborative projects involving clinical and laboratory cancer research * A competent and friendly Biostatistics department...emerging from real-life applications   __Your duties:__ * Biostatistical consulting and collaborative support for various DKFZ research projects * Ensuri…

job biostatistics germany Job

updated 9.2 years ago • m.hummel

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...BiocManager") : 'lib = "/share/apps/rmodules"' is not writable Would you like to use a personal library instead? (yes/No/cancel) yes Wo…

software error bioconductor

updated 6.6 years ago • colin.kern

their core facility team as a staff scientist. ## You will: - Support IMB researchers and external collaborators in the planning, analysis, interpretation, presentation and publication of diverse NGS and other omics data...skills and proficiency in English ## Desirable qualifications: - Experience in interdisciplinary collaborations or bioinformatics services - Knowledge of machine learning m…

bioinformatics job germany

updated 4.0 years ago • sergisayolspuig

is at the Assistant or Associate Professor level and in either the Adjunct or In Residence series. Duties: Pursue an independent bioinformatics research program and be partially self-supporting with own and/or...collaborative grants. Liaise with basic, clinical, and translational science investigators who utilize contemporary high...action to assure equal employment opportunity for underutilized…

Microarray Microarray

updated 16.9 years ago • mark@biostat.ucsf.edu

Please see the following link for more details about how to apply: https://www.findaphd.com/phds/project/the-circadian-clock-in-the-ageing-plant/?p112907 Plants respond to environmental signals in a time-of-day dependent...plan their harvests even under unpredictable weather patterns caused by climate change. This PhD project will investigate how the genetic targets of the circadian clo…

transcriptomics gene expression time series plant biology circadian Job

updated 6.2 years ago • dezer

scientific programmer to produce software implementing techniques, explored in an existing project, in a manner that is suitable for use within production environments. S/he will also provide initial support to users...into further development of the AYB methodology. The scientific programmer will report to the AYB project leaders at the EBI and will collaborate with scientists at EBI and other r…

updated 16.5 years ago • Wolfgang Huber

Data Analyst who will conduct analyses of genomics data from childhood cancers in close collaboration with molecular biologists, geneticists, pediatric oncologists and other bioinformaticians. Current projects...of experimental model systems. __You will:__ * __Lead the bioinformatics analysis of genomics projects in all stages from the experimental  planning to data interpretation, v…

bioinformatician job computational biology cancer genomics job Job

updated 9.3 years ago • Max Kauer

<h2 id="the-institute-of-molecular-biology-ggmbh-funded-by-the-boehringer-ingelheim-foundation-is-recruiting-a-staff-bioinformatician-m-f-">The Institute of Molecular Biology gGmbH funded by the Boehringer Ingelheim Foundation is recruiting a Staff Bioinformatician (m/f)</h2> The Institute of Molecular Biology (IMB) is a Centre of Excellence for Life Sciences, funded by the Boehringe…

bioinformatician germany Job

updated 7.5 years ago • sergisayolspuig

div class="preformatted">Dear List, I was using maSigPro for time series analysis of microarray. I have about 12 time points for a yeast data, and each time point only has two replicates...overfitting become a problem? I noticed that in maSigPro tutorial, 4.4 mentioned "Long Time Series". But it has no detailed explaination. Does Ana or someone can share&a…

Microarray Yeast Microarray Yeast

updated 15.4 years ago • Xiaokuan Wei

Hello, I'd like to make clear how the 'Heat Map for Genes in Dataset' which is one of plots in the '(project name).global.plots.pdf' and is generated by the Gene Set Enrichment Analysis R code (GSEA.1.0.R)? The code is available...set which is somehow normalized and the columns are grouped according to the lables provided by the person running the code. My question is how the rows in the heat ma…

Genetics Clustering DECIPHER Genetics Clustering DECIPHER

updated 15.8 years ago • Radek Blatny

for us to communicate with each other about developments and issues related to the Bioconductor project. A first request: Please send Jianhua Zhang (jzhang@jimmy.harvard.edu) a URL for your personal (professional) web page...provided in inst/docs/xxx.tex. Once we can do this I think we should release in beta form. Third: Duncan Murdoch has built R1.4 for windows…

Biobase annotate Biobase annotate

updated 24.1 years ago • rgentleman

normalize gene counts. However, I am concerned that this normalization may be problematic for time series data in which counts may increase over time across samples. Have the developers taken this into account when analyzing...time series data, and is there a suggested method for normalizing count data across samples for time series data

DESeq2 Normalization Medianofratios

updated 4.8 years ago • Joshua

Fellow Bioconductors, Anyone looking for a position that involves a lot of Bioconductor and cancer genomics may be interested in this opening: \*The Position\* The department of Bioinformatics and Computational Biology is seeking a computational biologist with proven experience in the comprehensive analysis of large, multi-dimensional, genomic datasets. This person will be a member of a highly co…

Job Sequencing Genetics Cancer

updated 11.3 years ago • Michael Lawrence

IMB researchers in the computational analysis of genomic data generated in the course of research projects. We are looking for a highly motivated Bioinformatician (m/f) with enthusiasm for academic research to join our team...and support a newly formed Collaborative Research Centre, CRC 1361, on the topic “Regulation of DNA Repair and Genome Stability”, funded by the German...Foundation DFG (see …

bioinformatician job Linux NGS Job

updated 7.1 years ago • l.brown

for both, basic research as well as therapeutic approaches. The aim of an intersecting, joint project of the Institute of Molecular Biology gGmbH and the University Medical Center together with a partner from the...7500 employees, healthcare, research and teaching are intrinsically linked. ### __To complement our project team, we are looking to fill the position of a Bioinformatician (m/f)__ T…

job bioinformatics germany Job

updated 8.3 years ago • sergisayolspuig

This position will allow the successful candidate to participate in several focused research projects and be involved in the analysis of large next-generation sequencing data sets, as well as studying mutations and...their impact on evolution and disease. This project is a collaboration with Professor Gil McVean (Statistical Genetics, the Wellcome Trust Centre for Human Genetics...is 12.00 midday…

Sequencing Genetics Sequencing Genetics

updated 11.8 years ago • Steve Taylor

http://gehlenborglab.org/) for additional information about our work.   Possible research projects include development of data visualization, analysis, and management tools to study genomic structural variants...for viewing and interacting with provenance graphs. All of the projects are highly interdisciplinary and are being conducted in close cooperation with computational or experime…

bioinformatics bioinformatician job data visualization Job

updated 10.2 years ago • Doe, Aimee

and cancer research. The successful applicant will have the opportunity to work on a wide range of projects with collaborators at the institute. Interested applicants should **submit their application online** at the link...a search for an experienced Master’s level Computational Biologist or Biostatistician. This person will collaborate with medical and basic science researchers in design, pi…

job biostatistics data science genomics Job

updated 6.7 years ago • Patrick Kimes

at="" yahoo.com=""> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] Long Time Series analysis > > Dear List, > > I?was using?maSigPro for time series analysis of microarray.?I > have about 12 > time points...is enought. > > I noticed that in?maSigPro tutorial, 4.4 mentioned "Long Time > Series". B…

Microarray Yeast Microarray Yeast

updated 15.4 years ago • Maciej Jończyk

variables of interest Time and Treatment. I also have a covariate of interest recorded for each person and timepoint, measuring a phenotype as a continuous variable. Call the variable P. I have been considering using the...primary contrasts of interest would be the Treatment:Time interaction (impact of treatment during a series of 4 baseline, 4 experimental, plus 4 recovery times), and the re…

limma spline design and contrast matrix covariate

updated 10.4 years ago • Hilary

<div class="preformatted">Hi, I'm looking to classify microarray data that comes in time-series measurements (3 time points per class). To my knowledge, there is no package in Bioconductor that supports classification of time-series data? If someone should know about such a package, or can hint me in the right direction of a non-BC package, that would be...div class="preformatted">Hi,…

Microarray Microarray

updated 18.9 years ago • Piet van Remortel

is preferred but not strictly required. Strong communication skills and a willingness to collaborate and to teach on an undergraduate and graduate level is a must. We expect good proficiency in English, and at least...equality of opportunity for men and women and therefore expressly encourages women to apply. Persons with severe disabilities will be given preferential consideration in case of equ…

updated 12.9 years ago • Stefanie

Bioinformatics supports researchers in performing data processing, basic analyses and high-level collaborations, as well as by providing infrastructure, teaching and consulting. We are looking for a Head of Core Facility...planning, data validation and functional analysis and provide support for grant applications - Collaborate with our scientists on several projects in parallel - Assess existi…

Epigenetics Infrastructure Epigenetics Infrastructure

updated 12.0 years ago • Holger Klein

**Introduction:** Sports injuries are an inherent risk for athletes, both amateur and professional, engaging in physically demanding activities. In Abbotsford, as in any other sports-centric community, the emphasis on preventing such injuries is paramount. Physiotherapy plays a pivotal role in not only rehabilitating athletes post-injury but also in proactively addressing potential risks. In t…

omada NestLink

updated 2.1 years ago • physiotherapytownline

of associated diseases. With the help of your PhD supervisor, you will drive a [DFG-funded research project][2]. You will investigate which epigenetic differences cause reproductive mole-rats to age significantly slower...communication skills **Our offerings:** - Challenging and varied tasks with a high degree of personal responsibility - A friendly and collegial environment - Extensive tra…

Mergeomics Epigenome Evolution NGS Aging

updated 21 months ago • arne.sahm

Strong written and verbal communication skills in English * Ability to work independently and collaboratively on multiple projects in parallel ## Desirable qualifications * Knowledge of software engineering and bioinformatics...workflows * Experience in interdisciplinary collaborations or bioinformatics services ## We offer * Stimulating, diverse and international research environment…

job bioinformatics germany Job

updated 8.1 years ago • sergisayolspuig

all, I have a question about the use of the frma function. I have to put several datasets from GEO series together in a same big analysis. However, for each of these datasets (that is each specific GSE serie) I have to select only...into a same Affybatch object and apply frma on this object -    For each GSE serie, first apply frma on all .cel files and then select…

frma normalization preprocessing

updated 9.0 years ago • ctruntzer

class="preformatted">Dear List, I have been thinking with using limma package to perform some time series analysis. There is a simple example in limma's manual. However, it seems that the analysis in the manual does not consider...the repeated measurement effect for time series data. I am wondering if limma has developed any method to deal with such time series data. Or I have to manually add…

limma limma

updated 14.5 years ago • Xiaokuan Wei

to check a few things, largely the design formula and potential issues with batch effect and time-series. Sadly our stats team is unfamiliar with these concepts and the tool as of yet and has helped as much as they can. The project

RNASeqData DESeq2 RNASeq

updated 23 months ago • island

Hi All, I have time series study, where colData files look like cellLine dex timeStep batch 200142521 TF-1 CTRL 24 A 200142571 TF-1 IFN-g 24 A 200142621...72 B The aim of the study is to find Significantly differential Expression gene across Time series 24, 48 and 72 hours. I have two replicates for each Time …

deseq2

updated 6.8 years ago • syednajeebashraf

diagnostic tests in oncology. These tests allow the molecular typing of cancers in order to personalize treatments for individual patients. IPSOGEN's major activities: -Oncodiagnostics: design, manufacturing, and...preclinical and clinical trials. Job Opening: Ipsogen has a position available for a Data Analysis Project Manager in its "Information Systems" department. Under the responsibility o…

Microarray Normalization Cancer Microarray Normalization Cancer

updated 19.1 years ago • Tagett Rebecca

div class="preformatted">Is there an easier way to do time-series correlation between genes of an ExpressionSet other than using for-loops and cor()? especially if I want to play with...the particular time-series? And I am not really happy with the packages I found so far: bioDist, qpgraph, qvalue I have: es...ExpressionSet ts <- c("t1", "t2...t3", "t4", "t5") some time series from e…

bioDist bioDist

updated 13.0 years ago • Forst, Christian

Aspects of Microarray Analysis (IV) June 18-23 2006, Bressanone-Brixen, Italy This 5 days lecture series provides an introduction to genomic data and their interpretation. The main focus will be on microarray experiments...Brown University (USA) The course is organized jointly by Universities of Milan and Padua, Italy in collaboration with the Biocondutor project and the R Foundation for Statis…

Microarray Proteomics Preprocessing Cancer Microarray Proteomics Preprocessing Cancer

updated 19.7 years ago • stefano iacus

__UPSCb__) is seeking a __staff bioinformatician __to consolidate its team. Among other projects, the UPSCb key to the deciphering of the Norway spruce genome, the largest sequenced genome at the time of publication...This, and other, project also prompted the development of a bioinformatics facility that has to date processed numerous Next-Generation...Sequencing based projects…

bioinformatician job next-generation sequencing sweden Job

updated 9.7 years ago • Nicolas Delhomme

Scientist - Full time and permanent to join our Research informatics group and contribute to our collaborative drug discovery projects, in support to translational, in vitro and in vivo biology departments, mainly in the...targets and contribute to the development of the platform. - Participation to RNA targeting projects - Communication of findings and presentation of results internally …

bioinformatics omics R oncology France

updated 4.1 years ago • vincent.piras

data from one project, the RNA from failed samples can be repeated to include into chips from another project (rather than running partial...chips to avoid wastage). Sometimes we include samples from other projects also. Here is a simple illustration Chip No ScanDate Contents 1 1st July *12 samples from project A* 2 1st July *8 samples...fro…

Normalization sva Normalization sva

updated 11.4 years ago • Adaikalavan Ramasamy

I am a college student in Arizona and I was wondering if anyone could suggest a topic for a course project (fall semester) using R / Bioconductor? I'm an experienced programmer (Perl, Python, Java, C, and some R) and I have completed...http://www.maricopa.edu/curriculum/A-C/116bio283.html I would prefer to submit an independent project in the area of cancer research. Any constructive feedback w…

updated 13.5 years ago • Caitlin

div class="preformatted">Dear Ozge, See Section 8.8 (Time Series Analysis) of the limma package User's Guide. I'm not sure how convenient you'll find it if you are a beginning user, but the...08 +0200 >From: Ozge Gursoy-Yuzugulu <sehriban at="" bilkent.edu.tr=""> >Subject: [BioC] time series analysis >To: bioconductor at stat.math.ethz.ch >Message-ID: <a06…

limma limma

updated 18.8 years ago • Gordon Smyth

<div class="preformatted">Hi R-Users and Developers, Several months ago I made a request on Sourceforge to add the R/S - programming language to the _Trove_ categorization. ("The Trove is a means to convey basic metainformation about your project.") Today I got the following response of one of the sourceforge admins. <snip> SourceForge.net will consider the inclusion of a programm…

updated 21.1 years ago • witek

MSc in Bioinformatics at the University of York.** You will develop a portfolio of bioinformatics projects, starting with a well-structured gene expression analysis project, followed by a research project that uses single...cell RNA-seq data and gene network inference, and finally ending with a third research experience on a topic of your choosing within the context of a biology lab. This yea…

bioinformatics JobPosting

updated 19 months ago • Daphne

Aspects of Microarray Analysis (III) June 19-25 2005, Bressanone-Brixen, Italy This 5 days lecture series provides an introduction to genomic data and their interpretation. The main focus will be on microarray experiments...in hands-on, interactive activities should consider signing up for the lecture and laboratory series (space is very limited; please read the NOTE below). These require a basi…

Microarray Proteomics Normalization Preprocessing Cancer Microarray Proteomics Cancer

updated 20.9 years ago • stefano iacus

Both of these systems are used in dozens of institutions worldwide. In addition to this project on patient linkage, there is a separate project in the Weber Lab to model the scientific workforce in order to understand...publications, 4 million patents, 2 million grants). Thus, there will be synergies between the two projects. __Requirements__: Candidates must have a PhD or other advanced degre…

Probabilistic Algorithms Big Data Job

updated 10.7 years ago • Doe, Aimee

please forward to them. Best regards and good luck to everyone, Michael O'Connell. BioConductor Project and Insightful Corp. Collaboration Announcement This week, Insightful Corporation announced the availability...of S+ArrayAnalyzer version 2.0, an updated module for S-PLUS based on collaboration with the BioConductor Project - a widely-used open source and open development software project for …

Microarray SAGE Annotation Infrastructure Microarray SAGE Annotation Infrastructure

updated 21.6 years ago • MOConnell@insightful.com

<div class="preformatted"> The Department of Biostatistics at Virginia Commonwealth University is seeking applicants specializing in genomic biostatistics for a tenure track position at the level of assistant (or associate) professor. Qualifications include: Ph.D. in biostatistics, statistics, bioinformatics, or related field. Candidates should have demonstrated experience in…

Pathways Bayesian Cancer charm Pathways Bayesian Cancer charm

updated 16.8 years ago • Kellie J. Archer, Ph.D.

from our community. We are seeking Outreachy interns who would like to work on a Bioconductor project, and mentors within the Bioconductor community to propose projects for Outreachy interns to work on during their...https://www.outreachy.org/apply][2] Feb. 24, 2023 at 4 pm UTC is the deadline to submit projects [https://www.outreachy.org/communities/cfp/bioconductor/][3] If you want help …

Bioconductor Outreachy community

updated 3.0 years ago • Maria Doyle

__UPSCb__) is seeking a __staff bioinformatician __to consolidate its team. Among other projects, the UPSCb key to the deciphering of the Norway spruce genome, the largest sequenced genome at the time of publication...Sequencing based projects. It also led to further development of essential community resources - hosted at UPSC - such as the Plant Genome Integrative...i) process…

bioinformatician job next-generation sequencing sweden Job

updated 9.7 years ago • Nicolas Delhomme

Hi everyone, Join us at Ensembl Job: Ensembl Genebuild Project Leader Please follow the instructions in the ad to apply (https://www.ensembl.info/2025/06/02/job-ensembl-genebuild...project-leader/) Closing date: 30 June 2025 All the best, Ensembl

JobPosting ensembldb

updated 6 months ago • Aleena_Ensembl

are very different. There is another reason why we generally > avoid analysing multiple projects together. The projects will usually need > to be submitted eventually to a public repository such as GEO, and the...QC the data from one >> project, the RNA from failed samples can be repeated to include into chips >> from another project (rather than runnin…

Normalization limma sva

updated 11.3 years ago • Adaikalavan Ramasamy

I am playing around with some test data and thought to add a third condition (let's just say A & B are treatments, C is the control) to try getting pairwise comparisons but am stuck on two...questions. 1) how do I get a lfcshrink for my third condition (i.e. A vs B) and 2) why does -log10p value vs log2 FC plot become flipped even though the reference is still C? Additional

DESeq2 volcanoplot deseq HELP contrast

updated 2.9 years ago • La

Hello! I am working with a single series time course data set looking at gene expression over a time series. My design is as follows Time Replicates Group uncut_1_i

maSigPro

updated 5.8 years ago • dorothy.mitchell

div class="preformatted">Dear all, the following student project is available at the EBI, Cambridge, UK. The project description is reproduced below. Regards, Gabriella -------------------------------------- Project title...its expression under each of the studied biological conditions and sample classes. This project is part of an ongoing effort of integrative analysis across very large coll…

Microarray Annotation Visualization PROcess Microarray Annotation Visualization PROcess

updated 16.2 years ago • Gabriella Rustici

Hi all. First things first, sorry for posting one more question about experimental design and time series in DESeq2. We have performed RNA-seq with two different treatments (control and protein over-expression) in two different...Hi all. First things first, sorry for posting one more question about experimental design and time series in DESeq2. We have performed RNA-seq with two different t…

DESeq2 design

updated 3.8 years ago • jordi.planells

Hello, I would like to use DeSeq2 to analyze time series data obtained using targeted RNAseq, instead of genome-wide RNAseq. These data are already normalized -- the need to...Hello, I would like to use DeSeq2 to analyze time series data obtained using targeted RNAseq, instead of genome-wide RNAseq. These data are already normalized -- the need to adjust...dataset. Is there a way to load…

series time targetedRNAseq

updated 3.0 years ago • Brynn

Bioconductor is participating in GSoC through the R Foundation this year. It looks like we have two projects: interactive graphics for scientific reports and extending mzR. Please see the R wiki for descriptions: http://rwiki.sciviews.org...doku.php?id=developers:projects:gsoc2014 IMPORTANT: the deadline for student applications (proposals) is TODAY. Michael [[alternative HTML version

mzR mzR

updated 11.8 years ago • Michael Lawrence

software we have developed. LabSynch is a fully integrated: - Electronic lab notebook - Web-based collaboration service - Sample tracking system - R-based data capture and analysis tool It is designed to help bench scientists

updated 19.1 years ago • John McNeil