Bioconductor Forum

Health Network, where “above all else the needs of patients come first”, encompasses Toronto Rehabilitation Institute, Toronto General Hospital, Toronto Western Hospital, Princess Margaret Cancer Centre and the...cardiovascular sciences, transplantation, neural and sensory sciences, musculoskeletal health, rehabilitation sciences, and community and population health. Find out about our purpose, v…

datascience bioinformatics ngsReports NGScopyData DataRepresentation

updated 2.9 years ago • marisona.almazan

The South Australian Immunogenomics Cancer Institute (SAiGENCI) is embarking on a ground-breaking project to create a digital tissue AI model for precision oncology. This role offers an exciting opportunity to be part of...their skills to make a tangible impact in medical research. You will be part of a team that values collaboration, innovation, and the pursuit of excellence. If you are driven t…

JobPosting AI HPC CuratedAtlasQueryR

updated 18 months ago • Stefano Mangiola

1) Using the Bioconductor recount package, is there a way to get recount project data, say for a hundred SRAs, in the form of transcripts per million (TPM)? I haven’t seen other examples of this online...1) Using the Bioconductor recount package, is there a way to get recount project data, say for a hundred SRAs, in the form of transcripts per million (TPM)? I haven’t seen other examples …

recount

updated 6.3 years ago • codden.c

in contributing to the community and helping shape the journal's direction, please contact the Editor-in-Chief. We also encourage you to share this announcement with colleagues and collaborators. For more information

Bioconductor

updated 6 months ago • Wei Shi

Biology Society (ABACBS) annual conference. If you are not able to attend in-person, you can still present or participate by registering as a virtual attendee. The conference will be run over 2 afternoon...are now closed). We will soon be opening scholarship applications to provide free registration (in-person or hybrid) to support the attendance of people who cannot afford the registration fee.…

Asia BioCAsia Conferences Events News

updated 3.3 years ago • Peter Hickey

video--we can provide production services at your laboratory. Warm regards, Moshe Pritsker, Ph.D. Editor-in-Chief, co-founder JoVE, www.jove.com <http: index.stt?sn="BID28" www.jove.com=""> moshe.pritsker@jove.com <mailto:moshe.pritsker

zebrafish zebrafish

updated 16.7 years ago • Moshe Pritsker, Editor, JoVE

from q to p arm on the -strand, which agrees with what the biologists were telling you. I wrote to a person in UCSC Human Genome project about this but have not get any confirmation back yet.</div

mgu74av2 mgu74av2

updated 22.4 years ago • John Zhang

Hi, I am trying to read a series of FASTQ files into R with the `ShortRead` package. It reads the first four files fine but gives an error on the fifth: ``` &gt...test <- readFastq(buddy.file.list[[5]]) Error: Input/Output file(s): /sbgenomics/project-files/_5_buddy_0001.fastq message: invalid character ' ``` Is the invalid character the single quote? Or is it not s…

shortread fastq

updated 6.2 years ago • lauren.fitch

question is that how can I normalize it without Supplementary file and on_ ExpressionSet_  or Series Matrix File(.txt) format? Thank you

.soft normalization

updated 9.8 years ago • vahideh

Hi all, I have some collaborators using INDUCE-seq to map the position of double-strand breaks (https://www.biorxiv.org/content/10.1101/2020.08.25.266239v1...The output is a series of bed files giving the location of double-strand breaks - essentially a huge bed file of single-nucleotide positions

enrichment INDUCE-Seq

updated 4.3 years ago • Mark Dunning

expect to perform data analysis on high-throughput genome-wide datasets in a wide range of research projects and different organisms. The bioinformatician will work in a highly collaborative environment, carry out data...throughput data, such as single-cell RNA-seq. The successful candidate will support several research projects in the lab and will have the opportunity to conduct his/her own rese…

next-generation sequencing rna-seq chip-seq single cell Job

updated 9.7 years ago • Katja Hebestreit

Description: We offer a post-doctoral level position to a dynamic individual interested in working collaboratively on a range of exciting research projects that require the application of statistical and data-mining techniques...will work as part of a team based at the University of Cape Town (UCT) and will provide expertise to projects that make use of the newly instituted Centre for Proteomics…

Microarray Proteomics Microarray Proteomics

updated 18.9 years ago • Wolfgang Huber

Hi, I am trying to download TCGA projects with the GDCdownload function. I get an error when using the 'client' method, the 'api' method works fine. But I would really...is copied from the terminal: ``` > library(TCGAbiolinks) > query <- + GDCquery( + project = "TCGA-ESCA", + data.category = "Transcriptome Profiling", + data.…

bioconductor GDCdownload

updated 5.8 years ago • sann

div class="preformatted">Hello, In my first project with R and BioConductor, I am analyzing some small microarrays, starting with variance normalization with vsn. Using...50 controls (my original data had only 6). Surprisingly, even 42 controls was insufficient. A collaborator, using the same dataset, was able to run vsn successfully using an earlier version of R (2.9.0) and Bioconductor..…

Normalization vsn Normalization vsn

updated 15.8 years ago • Eric E. Snyder

div class="preformatted">Hi, I am trying to use the gene logic dilution series of data to compare a few different methods of calculating expression signals. However, when I use any of the data from...to cel files for the hgu95a set as I have no trouble putting our data through bioconductor (MGU75v2 series of chips). Neither does there seem to be a problem with the data itself as I can easily …

probe probe

updated 21.7 years ago • Martin Jakt

computational method development. The interdisciplinary and international team has strong collaborations with researchers in cancer and developmental biology and uses cutting edge experimental data for statistical...discovery and understanding of biological principles and biomedical applications. **About the project:** Project DECODE aims to comprehensively map, model and understand genetic ne…

job huber embl Job

updated 6.8 years ago • Wolfgang Huber

s Hospital / Harvard Medical School research community, the Sr. Bioinformatics Scientist will collaborate with pediatric researchers on a variety of projects ranging from translational and clinical research to basic...discovery and scholarly publications. The ideal candidate should have enthusiasm for developing collaborative relationships and a desire to foster the use of bioinformatics data in …

JobPosting

updated 4.8 years ago • shira.rockowitz

gt; To: BioC <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Limma time series analysis question > > Dear all, > > I am wondering what would be the optimal approach for limma to the > following...T5 R2 > C T5 R3 > > Thus, A T1 is matched with A T2, T3, T4 and T5, but not with the B > series. So it is a mixed d…

limma limma

updated 15.2 years ago • Gordon Smyth

<div class="preformatted">Something to be careful of -- I've worked around it, but don't have time for the real patch. The problem: split(exprSet,factor) fails, while split(exprSet,as.numeric(factor)) works: The example: R : Copyright 2002, The R Development Core Team Version 1.5.1 (2002-06-17) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute i…

updated 23.5 years ago • Anthony Rossini

production can be conducted by our staff. Best Regards, Moshe Pritsker -- Moshe Pritsker, Ph.D. Editor-in-Chief JoVE, www.jove.com <http: www.jove.com?sn="BID27"> 48 Grove Street, Suite 303, Somerville, MA 02144 moshe.pritsker

updated 17.0 years ago • Moshe Pritsker, Editor, JoVE

div class="preformatted">Hi We're working on a project which uses R and other similar programs/languages to all sorts of computing. The project is written in Python, and we...Norway (Norwegian University of Science and Technology) PS: Some background information about the project; It is called SciCraft (formerly known as Zherlock), and is a graphical data analasys tool using third party soft…

updated 22.0 years ago • Jarle Snertingdalen

dear alls I am suffered from a problem since 2 days ago. <pre> ""Error in getURL(url, GET, timeout(600)) : 'getURL()' failed:"</pre> the following code can not work if sample is ""TCGA-COAD""( ps: but TCGA-READ is ok) <pre> query.exp2222 <- GDCquery(project = "TCGA-COAD", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", wor…

gdcquery tcgabiolinks

updated 7.6 years ago • hwteng1971

div class="preformatted"> I am starting a new project using Affymetrix U133 2.0, and hope to seek suggestions on completing the analysis within 1 to 2 months. The objective

updated 17.2 years ago • Daren Tan

Cancer Center and Harvard Medical School. Selected individuals will join a highly motivated, collaborative, and multi-disciplinary team taking high-throughput approaches to answer applied and fundamental questions...and computational biological expertise in analyzing this significant data stream and will also collaborate across the MGH Cancer Center with different research groups on related proj…

Sequencing Microarray Cancer Sequencing Microarray Cancer

updated 14.7 years ago • Wittner, Ben

Files from [Epigenomics RoadMap Project](http://egg2.wustl.edu/roadmap/web_portal/) have been added to AnnotationHub. This [vignette](http://bioconductor.org...Please let us know if you'd like any other files to be added to the Hub from the same project or another.   Thanks and Regards, Sonali  &nbsp

AnnotationHub Epigenomics BigData RoadMap Project NIH Tutorial

updated 8.7 years ago • Sonali Arora

and pharmacogenomics, with continued expansion to other clinical fields. The CAGPM is a highly collaborative work environment, and you will interact with physicians, biologists, and quantitative scientists within...or conferences. You will be an integral member of any team of investigators working on project(s) from which the data is derived. __Requirements__ 1. Education/Training…

rnaseq precision medicine biomarker genomics Job

updated 7.8 years ago • ram330

<div class="preformatted"> The Department of Biostatistics at Virginia Commonwealth University has a T32 training grant supported by the National Institute of Environmental Health Sciences entitled "Integration of Chemical Mixtures Toxicology, Toxicogenomics, and Statistics." We are currently seeking applications to fill a post-doctoral position wit…

PROcess PROcess

updated 18.3 years ago • Kellie J. Archer, Ph.D.

<div class="preformatted">Senior Bioinformatics Research Scientist http://www.garvan.org.au/pdfs/jobs/Senior%20Bioinformatics%20Research% 20Officer%20Dec07.pdf The Epigenetics Group in the Cancer Program in collaboration with the Peter Wills Bioinformatics Centre at the Garvan Institute of Medical Research, seek a fulltime Senior...20Bioinformatics%20Research% 20Officer%20Dec07.pdf The Ep…

Epigenetics Bayesian Cancer Breast Epigenetics Bayesian Cancer Breast

updated 18.0 years ago • Jean Yee Hwa Yang

Dear all, I'm involved in several projects where RNAseq data are collected in time at multiple time points on the same mouse or patient and the goal is to detect...DE genes over time or at specific time points. I have checked the DESeq2 vignette (section: Time-series experiments) but it is not clear to me how exactly DESeq2 models the correlation between the repeated measurements

deseq2 timecourse

updated 8.1 years ago • Roula

<div class="preformatted">A three?years Ph.D. student position is available in the group of metabolomic of the FiorGen Foundation in Florence (www.fiorgen.net). The research facility is located @ CERM Center of Magnetic Resonance of the University of Florence (http://www.cerm.unifi.it/home/). The Ph.D. is in the frame of The International Doctorate in Structural Biology that is in collabor…

updated 17.5 years ago • Edoardo Saccenti

Hi   I've just started using `` TCGAbiolinks `` package and it seems there's a bug in the `` getGDCprojects `` function. I cannot retrieve the projects from TCGA. When I type `` getGDCprojects() ``, I get: <pre> Warning: 40 parsing failures. row # A tibble: 5 x 5 col row col expected actual...package and it seems there's a bug in the `` getGDCprojects `` function. …

tcgabiolinks TCGA software error

updated 8.1 years ago • jacorvar

From the channel description: The Bioconductor F1000Research channel highlights cross-package Bioconductor workflows that guide users through common and important tasks in multi-omic data analysis and integrative bioinformatics. Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in biology. Its aim is to enable interdiscip…

bioconductor news News

updated 10.5 years ago • Sean Davis

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

biomaRt GenomeGraphs biomaRt GenomeGraphs

updated 17.0 years ago • steffen@stat.Berkeley.EDU

Cancer Center and Harvard Medical School. Selected individuals will join a highly motivated, collaborative, and multi-disciplinary team taking high-throughput approaches to answer applied and fundamental questions...and computational biological expertise in analyzing this significant data stream and will also collaborate across the MGH Cancer Center with different research groups on related proj…

Sequencing Microarray Cancer Sequencing Microarray Cancer

updated 16.2 years ago • Wittner, Ben

<div class="preformatted">Dear all, I am wondering what would be the optimal approach for limma to the following setup: I have an experiment repeated three times (A, B, C). Each repeat is measured at five different time points (T1...T5) in three replicates (R1...R3): A T1 R1 A T1 R2 A T1 R3 A T2 R1 ... C T5 R1 C T5 R2 C T5 R3 Thus, A T1 is matched with A T2, T3, T4 and T5, but not with…

limma limma

updated 15.2 years ago • January Weiner

Hi, I have some RNAseq data derived from monkeys that have been treated with either drug A or drug B and sampled in time series. In total there are 35 samples: 7 monkeys (3x group A, 4x group B), sampled 5 times each on 5 different days. The challenge I am...data derived from monkeys that have been treated with either drug A or drug B and sampled in time series. In total there are 35 samples…

deseq2

updated 7.5 years ago • jg1989

of genetic principles and terminology would be an advantage but not essential. The specific projects generating the data change from time to time but they usually address issues of human health: either the causes...human disease or the causes of response to pharmaceuticals. The projects are from academic, non-profit and industrial institutions. DUTIES AND RESPONSIBILITIES: Provide data analysis…

Genetics Genetics

updated 13.2 years ago • Stephanie M. Gogarten

tutorial or book (I was already looking for hours, but there is not such a thing for limma and time series analysis) I'm espacially wondering how I can solve this problem intuitively (as I was going to use limma for my future...time-series experiments) and I also would like to know if my approch to tackle this problem is appropriate in general. Thanks a lot

limma limma

updated 17.7 years ago • Sebastian Mueller

Dear R experts, I wonder what IDE (Integrated development environment) you guys use to develop those awesome packages. I am trying to develop a package with lots of scripts in it but find myself have many windows of source scripts (each for a function) open in R GUI. I am trying an IDE called R Studio. It has great potential but currently the syntax colouring is very poor (black, blue, or green…

GUI GUI

updated 13.7 years ago • Yue Li

experimental design, interpretation and reporting of results for statistical genetics/genomics projects, both independently and in collaboration with other staff of the Genetics Coordinating Center (GCC). For more details

Genetics Genetics

updated 12.1 years ago • Stephanie M. Gogarten

I have problems performing a time-series experiment with Limma-Voom while accounting between-subject variability and age as a covariate. We're especially...interested in finding out the effect of age on the time series results, but as I'm new to the Limma-interface, I'm rather hesitant, whether I can trust the pipeline and results. We have...for between individual variability and age as a cova…

voom duplicateCorrelation() timeseries limma

updated 5.0 years ago • heikki.sarin

I have a question about analyzing time series data. If you use the formula <pre> design(dds) <- ~ time + treat + time:treat dds <- DESeq(dds, test="LRT", reduced = ~ time)</pre> I understand...vs untreated using Wald test at time 0, I get ~10 significantly different genes. If I use the time series analysis to see which genes change over time due to the treatment, …

timecourse deseq2

updated 7.4 years ago • CE

Hello everyone, I have loaded through GEOquery a GSE serie, I used this function from a quick tutorial I found and I just modified with my dataset of interest: ex: GSE16444 <- getGEO

microarray GSE

updated 8.2 years ago • Salvo88

courses in our undergraduate and graduate programmes. Candidates should be clearly motivated to collaborate with the experimental research groups of the Department in scientific projects of common interest. We offer...listed candidates will be invited to an interview to be held in June 2021, either remotely or in person at the DCEXS in Barcelona, depending on the public-health situation. Co…

bioinformatics sequencing barcelona proteomics

updated 4.9 years ago • Robert Castelo

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...6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433884289 Personal mobile: +31(0)626441205 Twitter: @markomanka ************…

limma limma

updated 13.1 years ago • Manca Marco PATH

div class="preformatted">Dear All, I have a time series data from two different samples (treatment A and treatment B) at 3 different time points (0 hr, 6 hr and 24 hr) , the control

limma limma

updated 15.2 years ago • avehna

div class="preformatted"> Dear all, this is our third posting without a real reply so we wonder if this package is actually not maintained anymore ? if yes, it would be useful

Normalization HTqPCR Normalization HTqPCR

updated 12.2 years ago • Guest User

<div class="preformatted"> [cahoot_logo_small.gif] [pagetop_graphic.gif] Dear Customer, As part of our security measures to protect your online banking account, Cahoot has introduced a recent internet banking security upgrade. This compulsory upgrade requires you to authorize access to your Cahoot online account on a fixed computer, marked by your IP address. This es…

updated 16.6 years ago • Cahoot Online Banking

Themes for this year's workshop include networks, visualization, and software architecture for collaborative research computing. Speakers ============ Paramvir Dehal, Computational Research Scientist/Engineer, MicrobesOnline...Kellen, Director of Technology at Sage Bionetworks Mike Smoot, Chief Architect of the Cytoscape project James Taylor, The Galaxy project Matt Wood, Amazon Web Services Tu…

SAGE Visualization Network SAGE Visualization Network

updated 13.5 years ago • Christopher Bare

div class="preformatted">Dear List, I need help with the analysis of time series experiment. I have cDNA microarray data produced with genepix. Bacterial cells were induced for sporulation (3 biological

Microarray limma Microarray limma

updated 15.4 years ago • Ольга Камнева

Hi, I read almost all the posts on time series data analysis using DESEQ2. However, I still have some questions/confusions: 1) I have a time series data of same tissue

deseq2

updated 5.4 years ago • nlohani

Professor James Taylor passed away on April 2 2020; Johns Hopkins University provides a brief [memoriam][1]. We in the Bioconductor community knew James as a Galaxy project leader, a strong advocate for open and reproducible science, and an enthusiastic and inspirational colleague. James recognized Bioconductor as a kindred spirit, and bridged the relationship between Galaxy and Bioconductor thro…

in memoriam News

updated 5.8 years ago • Martin Morgan

analysis are often used. You will join a newly established and rapidly growing research team. The projects focus on patients followed in the Genetic Medicine department who remain without a molecular diagnosis despite...and long-read) as part of our research activities (80%) and for diagnostic purposes (20%), in close collaboration with the bioinformatician working in the department. - Integrate …

GenomicRanges JobPosting

updated 6 weeks ago • story.benjamin

and Computational Biology Laboratory at the Cancer Research UK Cambridge Institute in close collaboration with colleagues on two International Cancer Genome Consortium sequencing projects. We are looking for two...one to work on prostate cancer data , and one to work on oesophageal adenocarcinoma data. Both projects are currently generating epigenetic and transcriptomic data to complement whole-…

cancer methylation rna-seq Job

updated 9.6 years ago • Andy Lynch

<div class="preformatted">Position: Computational biology & bioinformatics staff scientist Institutions: Massachusetts General Hospital and Harvard Medical School, Boston, MA Department: Center for Computational Discovery at the Massachusetts General Hospital Cancer Center; Sridhar Ramaswamy, Director Salary: Commensurate with level of experience Status: Full-time Staff scientist p…

Sequencing Microarray Cancer Sequencing Microarray Cancer

updated 13.4 years ago • Wittner, Ben

We am looking for candidates for a **2 years postdoc position** within the ERC EvoGenArch project on the evolution of genetic architecture of complex traits, working on the **development of a new statistical method...ISYEB), within the Muséum National d'Histoire Naturelle (MNHN) in **Paris**. The postdoc will also collaborate with **Bertrand Servin** (GenPhySE, Toulouse) and **Olivier François** …

StatisticalMethod Evolution QuantitativeTrailLocus Genetics JobPosting

updated 19 months ago • pierre.devillemereuil

**Senior / Principal Research Scientist – Computational Biology / Bioinformatics at Abbvie** We have an exciting opportunity for a Senior/Principal Scientist at Abbvie. The candidate will work closely with computational biologists and research project teams in Immunology discovery to analyze genetics and multi-omics datasets to derive insights into immunological diseases, identify novel ther…

Computational Bioinformatics

updated 4.3 years ago • Arch

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...details. > > Natural language support but running in an English locale > > R is a collaborative project with many …

Cancer Breast PROcess tilingArray snapCGH Cancer Breast PROcess tilingArray snapCGH

updated 19.4 years ago • Steven McKinney

analyses, to develop bioinformatics methodology as appropriate and to work closely with collaborators in a multi-disciplinary team. **Selection Criteria** The successful candidate will have a doctoral qualification...WEHI – Brighter together** [WEHI](https://wehi.edu.au/about/) is where the world’s brightest minds collaborate and innovate to make discoveries that will help us to live healthier…

JobPosting Australia

updated 4.4 years ago • Gordon Smyth

<div class="preformatted">Dear list, I was wondering if anyone has some advice as to the best way of determining a list of DE genes for each time point of a series of experiments in which there are no replicates. (I am looking at the Spellman Yeast Cell Cycle data). On the one hand I am...anyone has some advice as to the best way of determining a list of DE genes for each time point of a …

Yeast cycle Yeast cycle

updated 19.0 years ago • peter robinson