Bioconductor Forum

pooled per group), but I understand correctly, during the actual snRNAseq experiment (done by a collaborator) there were four Illumina libraries prepped (one per group, same protocol for all done at the same time) and then...I applied MNN batch correction but realized that whether I applied it or not, my clustering and tSNE projections were virtually the same. Do I need to apply batch correcti…

BatchEffect SingleCellExperiment

updated 23 months ago • NeuroDaniel

started with just 28 people. Now, we are powered by 50,000 employees globally who nurture a diverse, collaborative and inclusive culture. **THE POSITION** A lot to do despite Corona! Boehringer Ingelheim is still looking for...RNAseq, scRNAseq) or genetics using established and innovative methods. - You contribute to projects during all phases - from experimental design to downstr…

R/Bioconductor Job

updated 5.4 years ago • nico.komarowsky.ext

relationships within the R&D and Operations teams. 5) Actively participate in developing project plans and providing regular updates against milestones 6) Collaborate with internal and external research scientists...with MySQL and public repositories of genetic, genomic, and biological data is a plus 5) Prior project experience with human genetics and/or analyzing data from genome-wide as…

Genetics Genetics

updated 13.4 years ago • Rong Chen

We, in the Lee Laboratory in the Sergievsky Center & Taub Institute at the Columbia University Irving Medical Center in New York City are seeking a highly motivated postdoctoral candidate(s) with formal training in Bioinformatics, Data Science, Statistical Genetics, or Genetic Epidemiology. A postdoctoral position is immediately available to work on a NIH-funded multi-center project on B…

JobPosting postdoc sequencing multiomics

updated 4.9 years ago • lhd

analytical pipelines to infer underlying molecular mechanisms. He/She will take a lead in the project management, data analysis and interpretation of results within the context of the biological problem being investigated...and will collaborate with other team members. The ideal candidate is expected to report the scientific results by writing scientific...papers and effectively communicate with …

Bioinformatics RNA-seq Postdoc Genomics Statistical model Job

updated 7.0 years ago • djawaheer

<div class="preformatted">Dear all, The following example in the package of knncat run well in R, so we hope to cluster our data just following this. The problem is how to import the data, how to build the vector and matrix? The first collumn should be the indentifier? the second collumn should be the expression average? and the third collumn should be the classifier? The data should be im…

updated 21.6 years ago • Liu, Xin

<div class="preformatted">Dear Ana, Your code should work already. Analysing log-ratios is the normal way to handle two-colour arrays. Please see the User's Guide which has plenty of examples. Best wishes Gordon > Date: Fri, 2 Oct 2009 15:00:08 -0700 > From: Ana Rodrigues <arodrigues at="" salk.edu=""> > Subject: [BioC] Using limma to analyze GEO datasets/ser…

Microarray limma GEOquery Microarray limma GEOquery

updated 16.3 years ago • Gordon Smyth

div class="preformatted"> Hello, Short summary version: How to interpolate a micro-array time series to get differentially expressed genes at a time point that was not measured? Long version: I'm analyzing a two species...human and mouse) and two groups (control and treatment) time series (9 time points) micro-array experiments using limma. For each species, I can contrast and test for differ…

limma limma

updated 11.8 years ago • Guest User

<div class="preformatted">Dear Bioconductor, We've just opened up a new position in Robert Gentleman's group. The title is Computational Biologist. Please see the description below. Genentech is an awesome place to work. Lots of cool computational and scientific challenges. URL: http://www.gene.com/careers/detail/00410610/Computational-Biologist The Position The Department of Bioinformati…

Infrastructure Infrastructure

updated 13.0 years ago • Michael Lawrence

<div class="preformatted">James W. MacDonald <jmacdon ...="" at=""> writes: > > I have two strains (B and W) and two different time points (2 and 1 hours). I am trying to find genes which > respond differently: > > 1. in B vs W, when comparing time points 1 and 2 (i.e. I compare BvsW in time point 1 to BvsW in time point 2) > > 2…

updated 17.7 years ago • Sanjat Kanjilal

Associate will also contribute to the integrative computational analysis of the resulted data. The project will provide an excellent opportunity to collaborate with a number of prominent labs that are taking part in the...nbsp; <strong style="line-height:1.6">Requirements:</strong> * A strong interest in conducting collaborative research on the topics outlined above * PhD degree…

Genomic Assays Chromatin Computational Biology Job

updated 11.2 years ago • Doe, Aimee

We are seeking a Senior Research Associate in Bioinformatics to undertake research for a Prostate Cancer UK and Movember Foundation Research Innovation Award study for the validation of the PUR (Prostate Urine Risk) test for prostate cancer. We have recently determined that cell-free RNA extracted from urine contains many prostate cancer gene transcripts which can be used to predict the state of …

cancer biomarkers bioinformatician Job

updated 6.1 years ago • Daniel Brewer

<div class="preformatted">Hi, I am planning to do RNA-seq on bacterial samples collected at different time points after treatment. I am just wondering, what should be the control of this series of samples, should it be untreated sample at time 0 right before the treatment, or should it be untreated samples at corresponding...at different time points after treatment. I am just wondering, wh…

updated 12.6 years ago • Yanxiang Shi

related funded research is required. Expected to be an asset in interdisciplinary health research projects in collaboration with the College of Health and Human SErvices and other health-related programs. A Ph. D. in Biostatistics...applicant will be expected to be, or soon become, a significant asset to interdisciplinary research projects in multidisciplinary medical and health related areas. …

Bayesian Survival Cancer PROcess ASSET Bayesian Survival Cancer PROcess ASSET

updated 23.1 years ago • Janusz Kawczak

Hi BioConductor community , I am working on a summer research project on GEO doing the following. Currently, anyone can look at the results of any previous study and ask if their mRNA under

GEOquery GEO

updated 18 months ago • gallantk5

was my first attempt > library("AgiMicroRna") > targets.micro=readTargets(infile="/Volumes/****/projects/****/ targets.txt") (sorry - paranoid collaborator) > dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) Error in readGenericHeader...function: > library("AgiMicroRna") > targets.micro=readTargets(infile="/Volumes/external/projects/LW/ targets.txt") &…

Normalization PROcess microRNA AgiMicroRna Normalization PROcess microRNA AgiMicroRna

updated 15.3 years ago • Mark Cowley

is an ETH core facility, created to enable and accelerate the execution of translational research projects by providing key technological resources, tools and collaboration opportunities for the personalized health...analyzing biological or medical data, for instance during a master’s thesis or equivalent work in a project, and strong programming skills in R. Ideally, (s)he also has experience wi…

job biostatistics bioinformatics data analysis core facility Job

updated 6.5 years ago • Michael Prummer

Hi, I am working with time-series RNA-seq data, and would like to make sure I have the right design for my purpose. The experiments like: <pre> Time = rep(c("0h...Hi, I am working with time-series RNA-seq data, and would like to make sure I have the right design for my purpose. The experiments like: <pre> Time = rep(c("0h", "2h

deseq2 timecourse design

updated 6.5 years ago • shao

__Direct Supervisor:     __Shiv Pillai, M.D. Ph.D. (pillai@helix.mgh.harvard.edu) __Email Contact:          __Vinay Mahajan M.D. Ph.D. (vinay.mahajan@mgh.harvard.edu)   __Employing Hospital and Department:        __ …

bioinformatician job bioinformatics immunology HIV Job

updated 8.8 years ago • Ragon Institute of MGH, MIT and Harvard

including The Cancer Genome Atlas (TCGA) and several International Cancer Genome Consortium (ICGC) projects. This project is affiliated to the UK ICGC Prostate project headed by Professor Ros Eeles at the Institute of Cancer...additionally involving PIs in Cambridge, Norwich, Oxford, St Andrews and Tampere.  __The Project __ This project is a mixture of methodology de…

mirna riboseq smallrna differential gene expression Job

updated 7.8 years ago • Andy Lynch

de-facto standard toolkit used in every clinical research lab for statistically informed analysis of personal multi-omic data. The use of the R programming language and the packages provided by the Bioconductor project has...of the GNU R software to handle big data becomes a bottle neck. BeDataDriven's task in the SOUND project will be to make our own interpreter for the R language, Renjin, comp…

job renjin reseach Job

updated 10.6 years ago • mj

Hi Aaron. I have Time-series bulk data (with two biological replicates for each time) and now I wish to use it to annotate my single-cell data. My Single...rep2 8 8hpi rownames(meta) <- meta$Sample_id bulk <- CreateSeuratObject(counts = c, project = "Time-Series") bulk$Sample <- "T-series" bulk$batch <- "T-series" bulk$batch2 <- "T-series" bulk@meta.data…

SingleR

updated 3.7 years ago • rohitsatyam102

I thank you about your guidances. But i still have problematic through import BigWig file or any Project as  project = 'SRP009615'. Despite that i check the version of "rtracelayer" that is (1.34.2 for bioc-release), furthermore

recount Tutorial

updated 8.9 years ago • Mustafa ABUELQUMSAN

passion, and creativity to improve the lives of people with serious diseases. Working in close collaboration with your Immuneering colleagues and with world-class R&D teams at leading pharmaceutical companies...the development of new medicines for diseases including neurodegeneration and cancer. You will see projects through from start to finish: experimental design, analysis of raw data,…

computational biology drug development genomics Job

updated 8.7 years ago • mmartin

have trouble to prepare the seed file. Just wondering whether you have any suggestions on which editor I can use to generate DCF format - Debian Control File on Mac. Thanks, Jia

software error BSgenome

updated 5.3 years ago • jiazhou0116

Please apply for this role at: https://careers-fhcrc.icims.com/jobs/28193/post-doctoral-research-fellow/job Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases. Based in Seattle, Fred Hutch is the only National Cancer Institute-designated cancer center in Washington. **…

JobPosting

updated 13 months ago • Fred Hutch (Recruiting)

The research group of Prof. Kirsi Pietiläinen at the Obesity Research Unit, University of Helsinki, located at Biomedicum Helsinki, is looking for a Postdoctoral Scientist. The translational lab Pietiläinen is focused on global metabolic profiling of obesity by systems biology methods, transcriptomics, proteomics, metabolomics and epigenomics, especially con-centrating on mitochondrial functi…

multiomics single-cell RNA Job

updated 6.2 years ago • mahes.muniandy

<div class="preformatted">Dear all, Im sorry if this is a question not directly related to using bioconductor packages, but at least I used them for the analysis that I need a reference to ;o) I have a biopsy related project with 63 unpaired biopsies in total and two groups where I cannot find any differences using limma, probably due to tissue heterogeneity. I wonder if there is anyone w…

limma limma

updated 17.5 years ago • Johan Lindberg

it under 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 in publications

updated 21.7 years ago • witek

__Bioinformatics Data Analyst in Cancer Immunology , __Research Institute of Molecular Pathology The Research Institute of Molecular Pathology (IMP) in Vienna is recruiting a bioinformatics data analyst for a collaborative research project focused on the discovery and pre-clinical analysis of candidate therapeutic targets for cancer immunotherapy. Strategies aimed at re-arming tumor-specific T c…

job NGS Data Analyst Cancer Job

updated 9.9 years ago • Jaritz,Markus

lab__](https://www.jax.org/research-and-faculty/research-labs/the-banchereau-lab)). This is a highly collaborative environment with multiple projects in the field of Immunology and Cancer. Analyst is expected to collaborate...cluster). Role will be directly supervised. Manager will determine assignment and prioritization of projects, as well as assessment of progress on projects, in direct consul…

rnaseq atac-seq iso-seq chipseq Job

updated 8.1 years ago • tyler.chukwu

17th June 2019. We seek a talented and highly motivated data analyst to join our exciting project applying artificial intelligence methods to understand cancer progression. The project will be based at the Systems...datasets in order to understand cancer progression and to develop early detection approaches. The project will utilise datasets generated by our experimental collaborators as well …

cancer deep learning genomics Job

updated 6.6 years ago • Shamith.Samarajiwa

Hello, I just noticed that biocLite() does not have all the default functionality of update.packages(). I'm switching over to mainly using a personal library instead of the R home library because of the recent changes in Windows Security Control and the wisdom of...not have all the default functionality of update.packages(). I'm switching over to mainly using a personal library instead of the R …

bioclite package updates

updated 10.8 years ago • Jenny Drnevich

<div class="preformatted">Hi, I have been asked by Professor Luisa Bernardinelli to re-advertise the below workshop on proteomics and metabonomics, which takes place at the end of March 2007 in Pavia, Italy. Regards, Brian Tom ========= What: A five-day workshop on the "Statistical Analysis of Metabonomic and Proteomic Data", as part of the Molecular Phenotyping to Accelerate Genomic …

Proteomics Proteomics

updated 18.8 years ago • Brian D M Tom

and finally the follow-up samples from visits 1, 2, 3 came in and were sequenced in the third batch. Here is an example of the meta data matrix: | patient| visit | batch| | -------------| -----------| ----------| | s1 |0 |baseline | | s2 |0 |baseline_resq | | s1 |1 |follow-up | | s3

duplicateCorrelation limma BatchEffect

updated 4.9 years ago • Julia

typically in a clinical setting. Furthermore, this bioinformatician will be involved in a project on the automation of literature mining in order to recommend treatment options. NEXUS collaborates with various...or a related field, and has demonstrated experience in biomedical, genomics, or integrative research projects involving high-throughput molecular data sets. He or she is familiar with hig…

clinicaldata translational genomics diagnostics research Job

updated 9.4 years ago • Daniel Stekhoven

the meningococcus) (<http://www.hrc.govt.nz/funding-opportunities/recipients/dr-philip-carter>). The project shall analyse whole genome sequencing data from clinical isolates to investigate the evolution, diversity, and...be based within a multidisciplinary team in the Health group of ESR, Wellington, New Zealand. The project is in collaboration with Professor Martin Maiden (University of O…

bacteria evolution population genomics Job

updated 8.5 years ago • una.ren

passion, and creativity to improve the lives of people with serious diseases. Working in close collaboration with your Immuneering colleagues and with world-class R&D teams at leading pharmaceutical companies...the development of new medicines for diseases including neurodegeneration and cancer. You will see projects through from start to finish: experimental design, analysis of raw data,…

rna-seq computational biology cns disease gene expression data neurodegeneration Job

updated 8.3 years ago • mmartin

A postdoctoral position in translational bioinformatics and cancer immunotherapy is available in the Translational Immunoinformatics Laboratory (TIIL) directed by Jason Luke, MD and Riyue Bao, PhD, within the Cancer Immunotherapeutics Center (CIC) of UPMC Hillman Cancer Center. Projects are in the areas of translational bioinformatics and cancer immunotherapy, in particular, integrating multi-omi…

cancer immunotherapy translational bioinformatics Data mining Statistical modeling Job

updated 5.9 years ago • lhuang7

<div class="preformatted">Dear Matthew, Your question relates to the limma package. contrasts.fit() includes all information, including info on genes with missing values. You can use topTable() for example to rank genes, including those with missing values. However eBayes() does not compute F-statistics for genes with missing values. I agree that this is a restriction, but I don't have…

Microarray limma Microarray limma

updated 17.3 years ago • Gordon Smyth

Hello, I'm analyzing a time series RNA-Seq data with repeated measures on six different time points corresponding to pre-treatment, on-treatment and

rnaseq edger makecontrasts

updated 8.6 years ago • wangzhang1988

# Group Greeting Cards in R Are you looking for a fun and personalized way to celebrate a special occasion with a group of friends, family, or colleagues? Group greeting cards in R might be the perfect solution! With R's powerful data manipulation and visualization capabilities, you can create custom greeting cards that include messages and images from multiple contributors. Here's how it w…

CARNIVAL

updated 2.4 years ago • carterethan745

__Johns Hopkins Bloomberg School of Public Health__ __Department of Biostatistics__ __Post-Doctoral Fellowship Opening__ __Positions to begin Spring or Summer 2019__ __Applications Due: __<span style="background-color:transparent">Open until filled, applications will be reviewed on a rolling basis and those received by January 31, 2018 will receive priority.</span> <span sty…

job single-cell data science cancer genomics Job

updated 7.0 years ago • Stephanie Hicks

Institut Curie in the context of the GEPIG (Genetics and Epigenetics of Tumor, http://gepig.curie.fr) project, an integrated approach to profile Breast Cancer from model systems to biological resources. Project: This project...and analysis of large sets of data in particular using new generation sequencing approaches. This project brings together research groups from the Institute, covering a ra…

Sequencing Epigenetics Cancer Breast DECIPHER Sequencing Epigenetics Cancer Breast

updated 16.5 years ago • Joern Toedling

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

updated 12.2 years ago • A M Torres, Hugo

A junior faculty position (Research Associate) is available in the Schizophrenia Center at the Johns Hopkins School of Medicine. The center seeks a talented and highly motivated bioinformatic/biostatistic expert to pursue translational/clinical research projects related to psychiatric disorders, including but not limited to a) first episode psychosis project, and b) chronic schizophrenia and mood…

Bioinformatician/biostatistician position Job

updated 9.3 years ago • lfrank8

Hi, I am using WGBS methylation data from CEEHRC project through DeppBlueR package and visualise it using Gviz. First track is a HM450 probes. Second track is obviously the...bases sequence of the genome. Third track is WGBS .  <img alt="" src="https://scontent.fymq3-1.fna.fbcdn.net/v/t1.0-9/33920934_10157458796798206_4768360506920534016_o.jpg...background.title="darkgrey") # WGB…

deepbluer gziv

updated 7.6 years ago • helimelanie

line-height:1.6">A Postdoctoral Research Fellow position is available immediately to work on a collaborative project between the laboratory of Eric Holland and Hamid Bolouri in the ___Human Biology Division___ of...and visualization methods___ for large-scale, molecularly-detailed, patient timeline data and collaborate with an existing team of bioinformatics, software engineering, and data man…

visualization genomics personalized medicine systemsbiology js Job

updated 10.8 years ago • Hamid Bolouri

__General Description:__ A post-doctoral position is available to develop methods and data resources for R / Bioconductor to integrate complex, heterogeneous, and large cancer genomic experiments. This National Cancer Institute-funded project is a collaboration between Bioconductor team members at Hunter College (a senior college of the City University of New&nbs…

bioconductor New York Job

updated 11.1 years ago • Levi Waldron

and the need for more accurate tools to support clinical decision making. The long-term aim of the project is to spare tens of thousands of men each year from unnecessary invasive diagnostic procedures while minimizing...the risk of missing significant cancers. Specifically, this project will develop AI-based data science approaches to achieve the following aims: • Integrating genomic data sets …

PhD cancer deep learning computational biology Job

updated 7.1 years ago • Shamith.Samarajiwa

novel drug target discovery and drug development. The job holder will contribute to the Bioconductor project through participation in computational frameworks for multi-omic data analysis. Context The European Molecular...of innovative medicines and brands. Bioconductor is an open source, open development software project to collaboratively develop tools for the analysis and comprehension…

job Job

updated 9.7 years ago • Wolfgang Huber

breast and other common cancers [1] and the Markowetz laboratory on integrative systemic analyses [2]. Project: The function of the two transcription factors FoxA1 and estrogen receptor (ER) are key drivers of breast cancer and...order to better understand its role in susceptibility to disease as well as response to therapy. In collaboration with the laboratory of Jason Carroll at CRI existing Ch…

Transcription Genetics Visualization Network Cancer Breast Lung Transcription Genetics

updated 13.9 years ago • Florian Markowetz

doctoral research is open in the group of Prof Laurent Gatto at the UCLouvain (Brussels, Belgium) in collaboration with Prof Vince Carey at Harvard University (Boston, MA, USA) to develop the necessary infrastructure and statistical...have recorded diverging observations about the correlation of the measurements. The goal of this project is to develop and expand the Bioconductor infrastructure in…

proteomics genomics transcriptomics software Job

updated 6.3 years ago • Laurent Gatto

a broad range of genomic datasets and have knowledge in genetics and biology. Our team is very collaborative, and the ability to communicate ideas and results to other scientists is important. What You’ll Do Depending...on your interest, we have a couple of potential projects to work: Improve variant-to-gene mapping using epigenetics data Evaluate novel methods to identify biomar…

JobPosting job

updated 3.9 years ago • xinf

I need help with Time series testing using DESeq2. - I have 5 subjects given same treatment at 11 different time points (for each subject: single observation

deseq2 time course rnaseq design contrast

updated 8.8 years ago • prppmet

development of therapies as well as development of cancer early detection applications. This project will use integrative computational approaches and large biomedical data-sets to develop and apply computational...methods to understand the complex systems involved in cancer formation and progression. This project will bring together big data analytical, modelling, data-mining and visualisa…

cancer genomics deep learning computational biology Job

updated 6.2 years ago • Shamith.Samarajiwa

Hello, I am analyzing an RNA-seq dataset generated by a previous lab member and I have a question regarding DESeq design for a time-series analysis. The data was generated from a drug treatment performed in vitro (same cell line for all samples) and I have the...dataset generated by a previous lab member and I have a question regarding DESeq design for a time-series analysis. The data was gene…

RNASeq DESeq2 timecourse

updated 24 months ago • WS

predicted from whole transcriptome analyses). The other project will focus on the development of statistical and bioinformatics approaches for detailed analyses and understanding...of functional homologies and divergences of cells and their gene regulatory programs. We expect both projects to take a highly collaborative approach between each other and with the other members of the host labs. We a…

evolution single-cell development differentiation cool Job

updated 9.5 years ago • Wolfgang Huber

__Description:__ One postdoctoral position in cancer genomics are available at the Guo-Cheng Yuan Lab in the Department of Biostatistics and Computational Biology at Dana-Farber Cancer Institute/Harvard School of Public Health. The goal of the Yuan Lab is to develop computational approaches to analyze and integrate genomic data with the aim to elucidate systems-level gene regulatory mechanisms …

cancer computational biology rnaseq chipseq Job

updated 11.2 years ago • gcyuan

Hello I have a dataset composed by a time series of 4-time points, two treatments, and a time zero control. My interest is to identify **the differentially expressed genes...over time. Do you have any suggestion? Also, I followed the suggestion of [Deseq2 - Time-series data with 2 treatments and 1 control][1]. Here it was suggested to use the days separately, which I did too: ```…

deseq2

updated 6.9 years ago • Ale