Bioconductor Forum

I have time series data from two gene background: 1) if I want to compared 0 hour first in each background and then see how is the difference

deseq2

updated 6.4 years ago • Cindy

this kind of data an easy task. However, I think I do not understand exactly the lifecycle of GEO series data, and I would like to ask in this list for any hint on this behavior, so I could try to fix it. What I first did was to download...15] "NA.9" "cg00000807" "cg00000884" "NA.10" "NA.11" "NA.12" If I select an individual GSM in the series, and download it, the featureNames are ok. If I try …

PROcess GEOquery PROcess GEOquery

updated 13.5 years ago • Gustavo Fernández Bayón

any other way in which we can store the R outputs in standard formats which can be viewed in vi editor or any other editor...??? As my output data is quite large enough, the output scrolls over the screen and I'm unable to view it

updated 18.6 years ago • Ruma Sanyal

<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 Reports to: Director of the Center for Computational Discovery, Sridhar Ramaswamy Salary: Commensurate with lev…

Sequencing Cancer Sequencing Cancer

updated 13.9 years ago • Wittner, Ben

Hi I have not done a time series analysis before. We have 50 patients that have been vaccinated and we are observing 1 baseline timepoint and 3 timepoints

microarray

updated 9.6 years ago • chris86

seqc'. It includes gene-level read count data generated by the SEQC (SEquencing Quality Control) project, which is the third stage of the well-known MAQC project (a US FDA initiative). The SEQC/MAQC-III Consortium produced benchmark

seqc rsubread featurecounts subjunc ercc News

updated 11.1 years ago • Wei Shi

github.com/zellerino/BOAT---biological-ontology-analysis-tool> I am happy and thankful for every person that wants to be part of the project and bring it together to fruition.   Ivo

gene ontology go analysis gene set enrichment gene set analysis News

updated 8.4 years ago • ivozeller

Hi all,      I am having some trouble with expression sets created by the GEOquery package from GEO series matrix files. There seems to be a problem with parsing featureNames. I begin by downloading a series matrix file: <pre> data <- getGEO(GEO="GSE63252",destdir=getwd()) > eset <- data[[1]] > eset ExpressionSet (storageMode:…

geoquery

updated 10.7 years ago • knaxerova

<div class="preformatted"> Greetings, Bioconductor Users! We are getting ready for our 5th Bioconductor release (1.4), and the increase in packages (along with corresponding procedures and methods) is simply incredible. The watchword for this release is: "Improved Documentation" and I hope we can live up to it. At this point, we are tentatively looking at a May 4th release date. …

Visualization Cancer PROcess Visualization Cancer PROcess

updated 21.8 years ago • A.J. Rossini

Hi all, I am using DESeq2 and edgeR to perform DE analysis on paired samples on a dog cancer project. Sorry if the question is redundant but I can?t find one very similar to my case. I have been designing models with 2 factors...the paired samples). I used the model '~sample_id + condition? until now but I would like to add a third factor, the breed. Is that then correct to use ?~sample_id + br…

Cancer edgeR DESeq2 Cancer edgeR DESeq2

updated 11.4 years ago • Mathieu Bahin

D. Murdoch, P. Murrell, M. Plummer, B. Ripley, H. Schwarte, D. Temple Lang, L. Tierney, The R Project for Statistical Computing (Web Site), http://www.r-project.org, 1996- I'm not sure about wheter or not to include H. Schwarte...affymetrix oligonucleotide arrays. In G. Parmigiani, E. S. Garrett, R. A. Irizarry, and S. L. Zeger, editors, The Analysis of Gene Expression Data: Methods and Software…

affy affy

updated 22.7 years ago • Warnes, Gregory R

Hi all, I have some phosphoproteomics, time-series data that I would like to analyze. I have four conditions (Control, MutA, MutB, MutA+B) and my aim is to i) Identify which phosphosites

limma splines

updated 4.0 years ago • rina

<div class="preformatted">I have a short RNAseq time series dataset (two time pointsl T0 and TN) and I have two conditions Undrugged and Drugged. For each of the drug conditions the...div class="preformatted">I have a short RNAseq time series dataset (two time pointsl T0 and TN) and I have two conditions Undrugged and Drugged. For each of the drug conditions

RNASeq RNASeq

updated 13.1 years ago • Simon Knott

apply.bio.mx/job/2019-J04 **About BioMed X** The BioMed X Innovation Center is an exciting new collaboration model at the interface between academia and industry (Nat Biotechnol. 2015 33(1):20-1). At our center, distinguished...career scientists recruited from all over the world work jointly on novel pre-clinical research projects in the fields of biomedicine, molecular biology, cell biolog…

neuroscience data integration transcriptomics Job

updated 6.7 years ago • slezak

and to identify genes that confer resistance to chemotherapy and targeted anti-cancer therapies. - Collaboration with the other research groups in the Institute. The institute has ongoing projects that have generated large...transcriptomic and SNP data on sarcoma, breast cancer and colon cancer, and is developing new projects based on data mining and high throughput sequencing. The bioinformatics…

SNP Sequencing Genetics Cancer Breast SNP Sequencing Genetics Cancer Breast

updated 15.7 years ago • Audrey Kauffmann

Dear all, my time series experiment; I exposed my plant to light and harvest after 6 time points (0, 0.5, 2, 4. 8, 10h), therefore, I have the effect of the...is what is the correct command line to import my txi data file as a deseq2 dataset in a  time series experiment. Is the following one correct or not??? dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Condition +…

deseq2

updated 7.1 years ago • ahmedaalkarim

<div class="preformatted">Undergraduate Student Project Summer 2007 at the European Bioinformatics Institute (EMBL-EBI) on the Wellcome Trust Genome Campus in Hinxton, Cambridgeshire. FIND Functional INtegration of Data - the synapse and the brain: the application of computational biology to understand more about the proteins involved in synapse function in the brain. The FIND project wil…

Pathways BRAIN Pathways BRAIN

updated 18.9 years ago • Wolfgang Huber

joint with the [Bioinformatics Division][2]) at WEHI. The laboratory works closely with research collaborators on various cancer diseases, with a particular interest in identification of cancer stem cells and understanding...and will work on cancer genomics and statistical bioinformatics methodology development. Specific projects may involve RNA-seq, ChIP-seq, ATAC-seq, single-cell multi-omics, …

JobPosting

updated 4.2 years ago • Yunshun Chen

funded ongoing projects in pancreatic and colorectal cancers. We are a small, productive and friendly lab that puts a high value on team work...department of oncology within the University, which provides various opportunities to interact and collaborate with world class experts in clinical science, surgery, basic science and bioinformatics. The ideal candidate...will be a highly motivated s…

R USA Hopkins GI Cancer Epigenetics Job

updated 9.8 years ago • asharm37

div class="preformatted">Pathview now can plot/integrate/compare multiple states/samples or time series in the same graph. Please check Figure 6 - 7 for examples and Subsection 7.2 in the vignette for details. Graphviz view

Pathways graph Pathways graph

updated 7.9 years ago • Luo Weijun

datasets. . Build a strong relationship with key groups within Pfizer, and form strong, productive collaborations with academic groups and groups in companies outside of Pfizer. Qualifications The successful candidate...as QC, normalization and statistical modelling through tools such as R/Bioconductor . Knowledge of third-party and public domain software for the analysis of genomic data . Pract…

Transcription Sequencing Microarray Normalization Pathways PROcess Transcription Sequencing

updated 16.3 years ago • Alexandre Kuhn

computational genomics, medical statistics, imaging analysis, and/or computational biology. The project combines single-cell, multi-omic data with large-scale human genetics to investigate the cellular origin of amyotrophic...1]) showed that vascular and glial cells contribute to the dynamics of neurodegeneration and this project will aim to refine our understanding of cellular mechanisms, biomar…

ATACSeq multiOmicsViz scRNAseq JobPosting

updated 3.5 years ago • Sebastian Lewandowski

computational genomics, medical statistics, imaging analysis, and/or computational biology. The project combines single-cell, multi-omic data with large scale human genetics to investigate the cellular origin of amyotrophic...1]) showed that vascular and glial cells contribute to the dynamics of neurodegeneration and this project will aim to refine our understanding of cellular mechanisms, biomar…

SpatialData scRNAseq SingleCell Omixer

updated 4.0 years ago • Sebastian Lewandowski

own research, while also providing support to scientists involved in quantitative biology. Members collaborate closely with laboratory and field scientists and strengthen the design and analysis of in vivo and in vitro...at the Institute. The post holder will develop a programme of research in bioinformatics in collaboration with Institute scientists. He or she will also help maintain and develop…

Infrastructure Infrastructure

updated 12.8 years ago • Jan T Kim

<div class="preformatted">Hi, I am trying to replicate the results gained from the Affymetrix SNP 10K experiments in the cancer genome project (http://www.sanger.ac.uk/genetics/CGP/). The publicly accessible data files (ftp://ftp.sanger.ac.uk/pub/CGP/affy/) are found...trying to replicate the results gained from the Affymetrix SNP 10K experiments in the cancer genome project (http://www.s…

SNP Cancer SNP Cancer

updated 19.4 years ago • Daniel Brewer

Dear member of this community: Since I have involved in bioconductor community, I have got benefits from this sites, thanks a lot to this great community. developing R package for parsing multiple bed files in R, as my master thesis projects, and I have done first version of my package. To be honest, writing R package is the first things I've ever done so far in...this great community. develop…

r packages submission

updated 9.9 years ago • Jurat Shahidin

with metabolomics data, expression data, and genomics clinical data. Research Program: This person will be part of a laboratory focused on Cancer Genetics and will lead a project on genomic instability that should...provide a first author publication. This scientist will also be involved in other projects for comparative genomics and analyses/interpretation of various datasets: expression, meta…

Genetics Metabolomics Pathways Cancer Genetics Metabolomics Pathways Cancer

updated 14.3 years ago • Emilie Bard

Brighter together** [WEHI](https://www.wehi.edu.au/about) is where the world’s brightest minds collaborate and innovate to make discoveries that will help us to live healthier for longer. Our [medical researchers](https...who want to make a difference. And we are committed to ensuring they have the tools to flourish, personally and professionally. We are a community of researchers, students and…

JobPosting Australia

updated 4.5 years ago • Gordon Smyth

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 or R packages...Type 'q()' to quit R. WARNING: UTF-8 locales are not currently supported > options(STERM='iESS', editor='emacsclient') > library(reposTools) Loading …

GO PROcess GO PROcess

updated 21.1 years ago • Jenny Bryan

IS Project Manager/ Day/ 40 Hrs/ Channing Division of Network Medicine - (3133887) Description This position includes both project...clinical trials, and cloud computing. Our group is centrally involved with the Bioconductor project, a 20-year open source/open development effort in the domain of statistics and computing for genome scale biology

softwaredevelopment Job job cloudcomputing genetics

updated 4.9 years ago • Vincent J. Carey, Jr.

to lead on the analysis of the proteomics component of the Cancer-Research UK-funded Prostate ICGC project. This project has generated many types of molecular data for the patient cohort being studied, that sit alongside...somebody who can take those data and use them to improve our understanding of prostate cancer in a collaborative manner. The successful candidate will have access to career…

Multiomics Proteomics Cancer Statistics Bioinformatics

updated 3.4 years ago • Andy Lynch

in the next generation sequencing Pan-Prostate Cancer Group Initiative (http://panprostate.org) in collaboration with Dr Daniel Brewer and Professor Colin Cooper. The Pan-Prostate Cancer Group Initiative is a collaboration...to improve the understanding of prostate cancer and patient care. The first data release of this project will be from an unprecedented 2000 men containing whole genome se…

cancer nextgenerationsequencing prostate Job

updated 5.5 years ago • Daniel Brewer

I have time series data from two condition, like 0h, 2h, and 6h by treatment A and B. I want to know FDR different between A and B at 1h fold change

deseq2

updated 6.4 years ago • Cindy

of the Bgee analysis pipeline and of the BgeeDB R package. S/he will actively participate in the collaborative management of Bgee development. The postdoc will be expected to write methodological articles, e.g. on new...and present results in national and international conferences. The postdoc will be encouraged to collaborate in biology-motivated projects in the lab and in the department. …

rnaseq data integration single-cell pacbio across species Job

updated 7.8 years ago • bgee

maximise the benefits of Australia’s associate membership of EMBL and does so via research projects, infrastructure and training programs across Australia. The Lynn Group is one of 20 research teams that are being...the EMBL model. __Key Responsibilities__ * Play a leading role in the PRIMES project, a €12 million European Commission funde…

postdoc bioinformatics network analysis australia systemsbiology Job

updated 9.7 years ago • david.lynn

<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 with salary ranges from $…

Cancer Cancer

updated 18.0 years ago • Kellie J. Archer, Ph.D.

Dear Forum, I am working on a somatic signatures project and I would like to make somatic signatures of the 80 Uveal Melanoma samples on the TCGA site but I encounter some...Dear Forum, I am working on a somatic signatures project and I would like to make somatic signatures of the 80 Uveal Melanoma samples on the TCGA site but I encounter some problems...know they used the HG19 build available …

bsgenome readvcf tcga annotation somaticsignatures

updated 9.8 years ago • jolligoodfellow

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 or R packages

rstudio

updated 4.3 years ago • Fiona

<div class="preformatted">Dear Colleagues: The Department of Epidemiology and Biostatistics at the University of Texas Health Science Center, San Antonio (http://deb.uthscsa.edu/index.html) and the Computational Biology Initiative at the University of Texas at San Antonio have a new faculty opening for a bioinformatics statistician. This position is related to a major new joint multi-disci…

Microarray Microarray

updated 19.2 years ago • John E. Cornell, Ph.D.

a novel, multi-disciplinary entity of biomedical science. There are many exciting ongoing projects at iMIND. One of these projects that the successful candidate will immediately join is first episode psychosis...FEP) project. This project brings clinicians, basic science researchers, and data scientists together to study pathophysiological...genes and pathways whose dysfunctions would interfer…

post-doc data science multimodal brain disorders biostatistics Job

updated 7.0 years ago • hjaarop1

maanova. --Naomi At 11:44 AM 1/22/2008, greg lefebvre wrote: >Hi all, >I have received time series dataset which I could not control the >experimental design. > >And here it is. This is a 2 conditions time series (placebo

TimeCourse limma timecourse maanova TimeCourse limma timecourse maanova

updated 18.0 years ago • Naomi Altman

<div class="preformatted">MDS and PCA are exploratory analyses the latter accentuating difference. If you are trying to make a diagnostic then I would be pretty worried if your signatures were too specific to a very narrow protocol-- they might be biased. Bear in mind that the bias you describe is not in the biological samples (the real target) but in the protocol. Try quantile or loess no…

Microarray Normalization Microarray Normalization

updated 19.9 years ago • Stephen Henderson

UCLouvain is recruiting a Research Logistician in Bioinformatics - full-time with a permanent contract - for the Louvain Institute of Biomolecular Science and Technology (LIBST) - in Louvain-la-Neuve **Context and organization** The Research logistician in bioinformatics will be based in the Louvain Institute of Biomolecular Science and Technology (LIBST) and will be very close …

transcriptomics proteomics job bioinformatician Job

updated 6.8 years ago • Laurent Gatto

<div class="preformatted">-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, This is not a proper Bioconductor question, but I think this is a good forum to place my request. I am looking for a public/available dataset regarding to a Mutiple Series Time Course Microarray design, for which also Real Time -PCR data for a number of genes has been measured. Can anyone put...a good forum t…

Microarray Microarray

updated 18.7 years ago • Ana Conesa

nbsp;   Enhance/Maintain Bioconductor packages developed in house * ¥    Collaborate closely with PIs and their lab members on research projects including evaluating, selecting, and implementing...and grant applications * ¥    Participate in the oral presentation of all project findings and abstracts including participati…

See Senior Bioinformatician position Job

updated 7.8 years ago • Julie Zhu

of spatial omics, Olink (proteomics) and single-cell data at WEHI (Melbourne, Australia). This person will be working with me as part of the Advanced Genomics Facility to analyse data from a variety of cutting edge spatial...protein-profiling data. This is a great opportunity to analyse data from cutting edge technologies, collaborate with excellent biomedical scientists, and to work in a suppor…

Proteomics JobPosting SingleCell Spatial SpatialExperiment

updated 22 months ago • Peter Hickey

filterVcf (with prefilters) and readVcfAsVRanges to retrieve sample variant calls from my sequencing projects. I have not been able to filter on sample genotype data (e.g. read depth etc.) with these routines, so I implemented this...routine as a third step. <span style="line-height:1.6">Lately, as the number of calls and number of samples have increased, one step is getting

variantannotation filterVcf readvcfasvranges filterRules

updated 10.9 years ago • Sigve Nakken

## Research Associate (Bioinformatician) (Fixed Term) __Apply via[ http://www.jobs.cam.ac.uk/job/12962/](http://www.jobs.cam.ac.uk/job/12962/)__ --- Applications are invited for the post of a Post-doctoral Bioinformatician to work on a collaborative translational research project between the groups of Dr Matthias Zilbauer (Department of Paediatrics at the University of Cambridge, UK), Dr. Paul…

postdoc bioinformatician biomedical informatics bioinformatician job job Job

updated 8.9 years ago • kraiczy

like advice about software and appropriate approaches for clustering genes. I have results from a series of 45 cDNA arrays comparing RNA sample extracted from a hela human cell line. My collaborators have over- expressed

Transcription Clustering Cancer Transcription Clustering Cancer

updated 22.7 years ago • Gordon Smyth

I have been getting a lot of use out of Biostrings latley. My collaborator has a series of regulatory elements that have been randomly joined together randomly, then put into a t-cell

Biostrings alphabetFrequency letterFrequency

updated 6.2 years ago • marc.carlson

I am new to R ,i have been trying to write the gse series matrix data into a csv file and i am not getting the output in the proper way as i need . the result.txt below is generating

R

updated 6.5 years ago • cs18s003

Hi, I am using DESeq2 to analyze a (short) time series gene expression dataset. Does anybody know what is the advantage, if any, of using an LRT (likelihood ratio test) for differential

DESeq2

updated 13 months ago • Denise

data sets, with particular emphasis on gene expression and the regulation of gene expression. In collaboration with biomedical scientists, the laboratory works on cancer genomics and immune disorders. The successful...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…

Australia

updated 4.3 years ago • Gordon Smyth

for high throughput biological computing. The incumbent must have ability to collaborate on research projects and independently conduct analyses of big ‘omics data, primarily in healthcare and agriculture...duties across the project team. Assist in collecting performance measurements of software on different hardware architectures, collaboratively...Experience writing research articles and grant…

supercomputing bioinformatics VariantCalling healthcare Agriculture

updated 4.1 years ago • Jenny Drnevich

The McDermott Center for Human Growth and Development/Center for Human Genetics at the University of Texas Southwestern Medical Center at Dallas ([www.utsouthwestern.edu](http://www.utsouthwestern.edu)) solicits applications for a postdoctoral research position in __Statistical Genetics<a name="OLE_LINK2"></a><a name="OLE_LINK1"> & Genomics</a>__. The lab focuses …

bioinformatician/biostatistician position Job

updated 9.2 years ago • chao.xing

I have an RNAseq dataset that is a developmental time series across 13 time points with 4 biological replicates. I'm interested in identifying differentially expressed genes...I feel like there is a better way to run the model in DESeq2. There is no treatment between time series and running the model above in DESeq2 shows very few genes differentially expressed between biological replicates

deseq2

updated 11.0 years ago • stradermarie

revise them to R 4.1.0. Flexible hours. **Long Description** Harvard University offers two series of online courses, *[Data Analysis for Life Sciences](https://www.edx.org/professional-certificate/harvardx-data-analysis...with a total of seven courses. These are currently written for R version 3.6.3 and (for the second series) Bioconductor 3.10. The courses require an R programmer familiar wit…

JobPosting

updated 4.3 years ago • Colin

Hello All, I am working on time-series RNA-seq data. I have four individuals and collected RNA-seq samples for each individual at 4 different time points...Hello All, I am working on time-series RNA-seq data. I have four individuals and collected RNA-seq samples for each individual at 4 different time points (T1

time-series DESeq2 RNASeq timecoursedata TimeCourse

updated 2.4 years ago • Debebe

Hi   I have a time series RNA-seq data from multiple subjects -- 14 time points each for 11 subjects. I am interested in finding inter-individual

timecourse multiple groups edgeR

updated 8.1 years ago • BharathAnanth

Dear all, I am using DESeq2 to estimate fold changes of treatment versus control in a time series experiment (with biological replicates). I am a little puzzled about the standard deviations of the fold changes provided

deseq2 log2fc standard error timecourse

updated 7.9 years ago • Verena