Bioconductor Forum

<div class="preformatted">Bioinformatician-NGS The Campus Science Support Facilities GmbH (CSF) is a non-profit organisation providing scientific infrastructure to the institutions at the Vienna Biocenter. We are seeking an experienced Bioinformatician (m/f) to join the Next Generation Sequencing Unit. Major tasks will be the primary analysis of sequencing data, development of analysis p…

Sequencing Infrastructure Sequencing Infrastructure

updated 14.1 years ago • Ido M. Tamir

Some of you may remember [my post][1] requesting help loading very large time series single cell data set from the GEO for DE. I'm now struggling with a very different issue. I believe I may be performing...DE wrong and I'm hoping someone can help me. I have a time series of single cell expression data and what I'm trying to do is filter for the genes that are more variable across the time...seri…

edgeR timecoursedata

updated 16 days ago • petergrahamclark

The new group of Dr. Simon Anders at the __Centre for Molecular Biolog__y of the __University of Heidelberg__ ([ZMBH](http://www.zmbh.uni-heidelberg.de)) is researching bioinformatics methodology for big data in molecular biology. We develop novel statistical inference methods for various types of high-throughput sequencing assays, and novel tools for visual and interactive exploratory analysis o…

computational biology job bioinformatician job Job

updated 8.7 years ago • Simon Anders

cancer genomics. You will conduct analyses of genomics data from childhood cancers in close collaboration with molecular biologists, geneticists, pediatric oncologists and other bioinformaticians. Current projects...systems. The CCRI is also involved into several large-scaled national and international research collaborations. The position offers significant opportunities for independent an…

postdoc rnaseq NGS WGS bioinformatician job Job

updated 7.9 years ago • da.de

graph) > h<-hashtable() #i have created a hash table using hashtable() from the library(graph). THIRD STEP: > for (i in 1:2512) > h[[map2Probe[i,1]]]<-unlist(strsplit(map2Probe[i,2], "\\;")) #this populate the hash table with each element...191 58952 Mobile: +358 44 023 5780 Lab WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/ Personal WebPage: h…

updated 20.1 years ago • Dario Greco

hello, I have a time-series, two factor design that I would like to analyze with DESeq2. The factor levels are: **Genotype** (wt, mut) **Tissue_age** (old, young

DESeq2 MultipleFactors TimeSeriesExperiment

updated 3.4 years ago • Maria

nbsp;Albany, NY   ### Duties and responsibilities: - Analyze next-generation sequencing data - Collaborate with research scientists to develop and implement cutting-edge data analysis pipelines for sequencing applications...necessary data analysis-related documentation - Plan, coordinate, and carry out activities in collaboration with research projects - Participate in the va…

bioinformatician job bioinformatics job Job

updated 8.7 years ago • ualbanybioinfo

I have problems performing a time-series experiment with DESeq2 while accounting for age as a covariate. We have one group with each individual having three...combination of each other based on the DESeq2 vignette. Does anyone have solution how this time series experiment could be done so that age could be accounted for? Was wondering that would replacing SUBJECT_ID with AGE

DESeq2 DES

updated 5.1 years ago • heikki.sarin

Hi Bio Conductor community , I am having trouble creating Series RNA-seq normalized counts matrix files that are the same as the ones on GEO. I know that these matrix files are already

GEO rnaseqGene RNA

updated 18 months ago • gallantk5

The German Cancer Research Center (DKFZ) offers a Postdoc position in the computational genome biology group headed by Dr. Bernd Fischer. The research group works on quantitative analysis of genetic and physical interaction networks. Statistics and computational network analysis will be used to predict and understand interactions between genes, proteins and drugs in various ways wi…

jobs computational biology cancer Job

updated 10.2 years ago • Bernd Fischer

Illinois. I installed R, perl-bioperl and perl-bioperl-run for a couple researchers who are doing collaboration using these tools. I was asked to install Bioconductor packages. I took a quick look at the installation notes...packages? If I install these packages as root will they be available to other users? Or will each person have to install Bioconductor packages themselves? I think I see …

Network Network

updated 17.2 years ago • Anthony Mullen

Bioc2020 is proceeding with planning for the conference to be held July 27-31, with contingency planning for an online-only conference if necessary. https://bioc2020.bioconductor.org/ As part of the program we want to encourage community involvement and interactive projects. This may take the form of birds-of-a-feather discussion topics (like an open forum discussion) but could extend to id…

conference bioc2020 talks deadline News

updated 5.6 years ago • shepherl

respectively, in our undergraduate and graduate programs. Selected applicants will be expected to collaborate with the other research groups of the department in scientific projects of common interest. Additionally, the...listed candidates will be invited to an interview to be held in May 2022, either remotely or in person at the DCEXS in Barcelona, depending on the public-health situation. Pl…

bioinformatics genomics proteomics biologicalchemistry sequencing

updated 4.0 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)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ************…

KEGGSOAP GEOquery KEGGSOAP GEOquery

updated 15.0 years ago • Manca Marco PATH

__The ____Computational Systems Pharmacology__ research group (<http://cosphar.utu.fi/>) led by Dr. Jing Tang focuses on developing and applying mathematical and computational tools to tackle biomedical questions that may potentially lead to breakthroughs in drug discovery, such as 1) how to identify drug combinations that can be used to provide more effective therapeutic strategies for can…

systemsbiology network analysis drugvsdisease Job

updated 9.6 years ago • jing.tang

Dr. Akira Sawa).** We seek a talented and highly motivated data analyst to join our exciting projects in translational brain study. We welcome people experienced in data analysis in fields such as neuroscience, genetics...test scores, guided by faculty members with expertise in data science ● join exciting research projects and perform statistical analysis, guided by project leaders ● provi…

RNAseq R Next-Gen Sequencing Imaging Brain Job

updated 6.8 years ago • hjaarop1

Director: Dr. Akira Sawa). We seek a talented and highly motivated data analyst to join our exciting projects in translational brain study. We welcome people experienced in data analysis in fields such as neuroscience, genetics...test scores, guided by faculty members with expertise in data science ● join exciting research projects and perform statistical analysis, guided by project leaders ● p…

data science research assistant brain disorders multidisciplinary bioinformatics Job

updated 7.0 years ago • hjaarop1

CBRG), based at the Weatherall Institute of Molecular Medicine (WIMM) in Oxford, UK. The CBRG collaborates with WIMM scientists to successfully integrate bioinformatics into their research. Working as part of the...team, the successful candidate will be the main point of contact for statistical and bioinformatics projects with a statistical component at the WIMM. The work will include applicat…

updated 12.4 years ago • Steve Taylor

CBRG), based at the Weatherall Institute of Molecular Medicine (WIMM) in Oxford, UK. The CBRG collaborates with WIMM scientists to successfully integrate bioinformatics into their research. Working as part of the...team, the successful candidate will be the main point of contact for statistical and bioinformatics projects with a statistical component at the WIMM. The work will include applicat…

updated 12.4 years ago • Steve Taylor

<div class="preformatted">Dear All, I carried out a time series analysis of a time course dataset using LIMMA method and I obtained a list of genes that change with time. However, I wonder...div class="preformatted">Dear All, I carried out a time series analysis of a time course dataset using LIMMA method and I obtained a list of genes that change with time. However, I

updated 17.2 years ago • yemi yomi

<div class="preformatted">Hi, Apologies if you have received this e-mail before. I have been asked by Professor Luisa Bernardinelli to announce the below workshop on proteomics and metabonomics, which takes place in March 2007. Regards, Brian Tom ========= What: A five-day workshop on the "Statistical Analysis of Metabonomic and Proteomic Data", as part of the Molecular Phenotyping to …

updated 19.0 years ago • Brian D M Tom

Hello, I am analysing Affymetryx and Illumina data from the MACQ project for the moment. I used the following commands to read and preprocess (normalisation, background correction,..) the Affymetry

microarray normalization Illumina data MACQ project gene expression

updated 6.7 years ago • naf

statistical methods to analyze these data for genetic risk, disease mechanism, and drug response. Projects may include network construction and mining. · Maintain complex next generation sequence and array datasets linked...regularly and contribute to the success of the research team. · Develop and maintain productive collaborations within Mount Sinai and with outside researchers in academi…

job postdoctoral fellow computational biology bioinformatics new york Job

updated 9.2 years ago • supindab

to analyze next generation sequencing data for genetic risk, disease mechanism, and drug response. Projects will include network construction and mining. * Integrate and translate genetic, genomic, eQTL, structural, and clinical...PI regularly and contribute to the success of the research team. * Develop and maintain productive collaborations within Mount Sinai and with outside researchers in…

genomics data integration job ngs computational biology Job

updated 10.6 years ago • supindab

to analyze next generation sequencing data for genetic risk, disease mechanism, and drug response. Projects will include network construction and mining. * Integrate and translate genetic, genomic, eQTL, structural, and clinical...PI regularly and contribute to the success of the research team. * Develop and maintain productive collaborations within Mount Sinai and with outside researchers in…

postdoc genomics Job bioinformatician computational biology

updated 10.4 years ago • supindab

CRISPR genome editing. We are active contributors to the open-source open-development Bioconductor project. We have developed more than a dozen packages with various utilities, ranging from machine learning, peak calling...software applications as well as providing bioinformatics data analysis support for various research projects. MAJOR RESPONSIBILITIES: * Develop novel algorithms and so…

single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job

updated 6.4 years ago • Julie Zhu

R/Bioc developpers to see what > other already did that seems to be suitable for a part of a project. Just a > word about tutorials, workflows and useful help in Bioc website; like every > bio* project (Bioperl, Biojava...Biopython..) when a project is lunched and > when people start to get involved in, there is always "how to do" sections > and lot of tutorials…

updated 15.1 years ago • Rick Frausto

[http://queensoftz.com/][1] [1]: http://queensoftz.com/

inveRsion

updated 3.3 years ago • rawoya6110

While reviewing the source code of your CRISPRseek package I am confused about one thing. While examining the buildFeatureVectorForScoring function, I saw that it was written differently in the source code I downloaded and the R program. I'm confused as to which one is the latest version. I would be very grateful if you could explain why this difference. In BuildFeatureVectorForScoring2 function…

CRISPRseek

updated 5.3 years ago • s.islambey

Hi everybody, I'm going to apply multiDE, an R package for detection of DEG in multiple treatment conditions, on some RNA-seq time series data... (I wanna assume each time point as a treatment condition) Let's assume Yidg denotes the normalized read counts for...multiDE, an R package for detection of DEG in multiple treatment conditions, on some RNA-seq time series data... (I wanna assume each …

RNA-seq Log-linear Main effects

updated 9.3 years ago • natalia.fghf

Hello, I am a computer scientist who is new at analyzing microarray data. So my question may be too easy so I apologize for that. I really need help with that. I got some dataset on GEO (GSE44248) on the human LCL cell line. I want to analyze this data using Limma to find differentially expressed genes. My data are time series and I want to find differentially expressed genes over time. Here is …

limma microarray time series DEG paired

updated 6.3 years ago • kawess

mechanisms i.e., genes affected by knock-down. Is 3 times points are enough to consider as time series data. Shall I do pairwise comparision of different time points or do time series analysis sing DESeq2. Here is an example

deseq2

updated 7.6 years ago • dryellaboina

Hi all, I downloaded the STAD project 450k methylation data. The version reported is "Data Release 39.0 - December 04, 2023"; the Samples dataset size is 397

MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData

updated 22 months ago • Giovanni Calice

Hi, I would like to know if there is any Bioconductor R package that can deal with RNA-seq time-series allowing for time offset between individuals. That is, I have 10 individuals, each with variable sampling (variable

edgeR deseq2 rna-seq timecourse fittimeseries

updated 7.5 years ago • jpsf

<div class="preformatted">Hi to all, I'm performing a time-series analysis on 2 cell lines with 4 time points, with 2 replicates at each time. I imported the data with "Affy" library, and I...div class="preformatted">Hi to all, I'm performing a time-series analysis on 2 cell lines with 4 time points, with 2 replicates at each time. I imported the data with "Affy" library, and

Normalization GO Normalization GO

updated 14.3 years ago • Andrea Grilli

I performing a Time-series experiment with several patients with 2 conditions and 2 time-points from each patient. The patients associated...I performing a Time-series experiment with several patients with 2 conditions and 2 time-points from each patient. The patients associated to...the differential expression between responders and non-responders taking into account both time-series. However, i…

DESeq2 RNASeqData

updated 3.1 years ago • perceval.vellosillo

2012); and a new mechanism to suppress aberrant exon formation (Zarnack et al, Cell 2013). *Ongoing projects* Ongoing projects address the following questions. All of these topics require the development of novel statistical...and biostatistics. People are given freedom to work on problems that interest them. *Wet/dry collaborations* The successful applicant will work closely with one of our c…

Cancer genomes Cancer genomes

updated 12.8 years ago • Kathi Zarnack

Hi, I would like to do a time-series analysis in DESeq2. I have following experimental design: Genotype: RR, SS Time: 0, 1, 7, 20 days There are 6 biological replicates

DESEQ2 timecourse multiple time points time

updated 8.6 years ago • ofonov

## Job description We are searching for an experienced **Research Software Engineer** to contribute to the development of the open-source software project “GSVA: Optimizing Gene Set Variation Analysis for Single-Cell Data”, funded by the [Chan Zuckerberg Initiative (CZI)][1...Research Software Engineer** to contribute to the development of the open-source software project “GSVA: Optimizing Gen…

JobPosting Devel GSVA Software

updated 3.2 years ago • Robert Castelo

<div class="preformatted">Functional genomic analysis of cancer/RNAi screening NATIONAL CANCER INSTITUTE, BETHESDA, MD The laboratory of Dr. Natasha Caplen, within the Genetics Branch, CCR, NCI, is seeking postdoctoral candidates for a project focused on functional genomic analysis using RNAi screening approaches. We are looking for a highly motivated candidate...Dr. Natasha Caplen, within…

Transcription Sequencing Genetics Pathways Cancer Prostate Transcription Sequencing Cancer

updated 14.3 years ago • Sean Davis

science-m-f-d/ **Location**: Dresden, Germany **Dewpoint Therapeutics** is building a highly collaborative team to harness the power of biomolecular condensates. Together, we are leveraging a transformative shift...efficient data processing workflows and provide general data analysis support across many different projects - Develop analysis pipelines making use of linear modelling and mult…

DataIntegration JobPosting

updated 4.7 years ago • António Miguel de Jesus Domingues

in Bioinformatics in the Cancer Genetics Team at Norwich Medical School, you will be part of a collaborative team of experts working on cutting-edge research to develop new biomarkers for cancer. You will have the opportunity...to work on a wide range of projects, gaining experience in a variety of areas, and working with leading experts in the field. Specific projects will include

JobPosting

updated 2.5 years ago • Daniel Brewer

# Bioinformatician (m/f) (\#CFBIO10) The __Institute of Molecular Biology gGmbH (IMB)__ is a Centre of Excellence for Life Sciences funded by the Boehringer Ingelheim Foundation and located within the campus of the University of Mainz in Germany. IMB focuses on epigenetics, DNA repair and developmental biology and offers premium scientific core facilities (see [www.imb-mainz.de/core-facilities](…

bioinformatics germany job Job

updated 9.2 years ago • sergisayolspuig

<div class="preformatted">hello R-users, I'm trying to do time series analysis using the samr package. I have an excel sheet with 25 columns and 22811 lines. the first row has the names of the...div class="preformatted">hello R-users, I'm trying to do time series analysis using the samr package. I have an excel sheet with 25 columns and 22811 lines. the first row has the names of

convert convert

updated 16.8 years ago • Assa Yeroslaviz

is an image of the plot][1]Hello World i have to predict the future using deep learning "LSTM time series Forecasting using Keras, i have a dataset of COVID-19 related to india where the no. of deaths and some other features...import Sequential from keras.layers import Dense from keras.layers import LSTM # convert series to supervised learning def series_to_supervised(data, n_in=1, n_out=…

#deeplearning #python #lstm #machinelearning

updated 4.1 years ago • AbuZar

<div class="preformatted"> Hi all, A computational biology position is open at Vertex Pharmaceuticals and is described below. If interested, apply through the Vertex website or feel free to contact me directly. Thanks, Brian ------------------------------------- The candidate will support the biomarker and systems biology efforts at Vertex by using statistical analyses and data mining …

Proteomics Proteomics

updated 19.0 years ago • Brian Hare

biologists, human immunologists, and clinician scientists who come together to perform team-based projects, with each postdoctoral researcher leading her or his own project. Therefore, a good balance between independence...The position offers a stimulating and multi-disciplinary environment with numerous opportunities to collaborate with researchers within and outside of the CTCN, including estab…

ComputationalNeurology

updated 3.6 years ago • Hans-Ulrich Klein

Hello, I have performed time-series experiments (3 biological replicates) in human cells. We want to identify differentially regulated genes at any time...with how the reference time point T0 is represented in the matrix. I am more of a wet lab person and my experience with R is a little less than moderate. I apologise in advance for the naive question, but any help here

limma time series help

updated 7.0 years ago • rm1238

are interested in improving their BioC/R coding skills and contributing to the overall BioConductor project. More details will follow shortly, but the meeting will feature a series of extended tutorials and workshops aimed

Sequencing Cancer Sequencing Cancer

updated 16.4 years ago • Crispin Miller

<div class="preformatted">Dear Group, Apologies for a similar re-post on this issue. I kindly want to bring to the attention of bioconductor developers, if there is a function to generate a heatmap of all enriched GO categories after a conditional hyperGTest. For example, I have 5 different time points time-series data and with 3 different doses. I run HyperGTest and I endup with atleast …

GO Visualization GOstats GO Visualization GOstats

updated 18.0 years ago • Srinivas Iyyer

are seeking a highly motivated, full-time Bioinformatics Data Analyst (m/f) You will work in close collaboration with research groups and the in- house Genomics department to analyse Next-Gen-Sequencing datasets, including...Candidates should have a strong interest in Life Sciences, willingness and ability to take project responsibilities and acquire project specific knowledge, as well as capac…

updated 15.8 years ago • Ido M. Tamir

strategy of CIAT. * Publish results in journals and at conferences. * Develop internal and external collaborations. * Develop projects and apply for funding. * The researcher will be expected to work with data from different...communication skills in written & spoken English, and the ability to speak Spanish is desirable. Personal Competencies: * Goal-oriented. * Dynamic, forward thinki…

Sequencing Annotation Sequencing Annotation

updated 14.4 years ago • Sarah Ayling

<div class="preformatted">Dear Bioconductor, Back in January, we announced an open position in Robert Gentleman's group, under the title Computational Biologist. While we have received many promising applications, the nature of the position has evolved over time, so we are restarting the process. If you applied before and remain interested, please restate your interest. URL: http://www.ge…

Infrastructure PROcess Infrastructure PROcess

updated 12.4 years ago • Michael Lawrence

Hello, I am trying to perform DGE analysis for a time series data. I am using DESeq2 for the analysis.  Upon searching the closes match I can get to what I am trying to do is here

deseq2 time course

updated 7.3 years ago • sum732

files[n], dec = TRUE) : Not a Codelink exported file. The first several rows of files are: PROJECT EXPERIMENT SAMPLE Sample001 DATE 2007-10-26T17:19:48 GENEID NCBI_ACCESSION TYPE_FLAG LO_ARRAY_ID EXPRESSIONVALUE...SPOT_COL SPOT_ROW SPOTMEAN SPOTMEDIAN BKGMEAN BKGMEDIAN ....... I emailed to the person from the company. They claimed that this txt file is from Code…

codelink codelink

updated 17.4 years ago • Diao,Lixia

wherever it exists. This drives our relentless search for the best science, and our pursuit of collaborations and partnerships. We believe there are no limits to what science can do. We are currently seeking post-doctoral...areas. * Help manage the delivery of scientific analyses in support of our R&D teams and collaborators within and outside Janssen. * Perform and publish high-quali…

Population Analytics Postdoctoral Fellow Job

updated 9.4 years ago • Johnson.Johnson.Careers

**About the role** We are seeking a talented computational postdoc to join the Secrier lab (https://secrierlab.github.io/) at the UCL Genetics Institute, where they will take the lead on an exciting project that aims to understand how genomic instability and complex structural rearrangements in cancer cells may lead to the development of metastases. The successful applicant will employ bioinfo…

cancer multi-omics genomic instability machine learning data integration Job

updated 6.8 years ago • msecrier

specific factors and molecular mechanisms underlying misregulation of the epigenetic states. The projects are being conducted in close cooperation with several experimental laboratories, providing an excellent opportunity...for collaborative research.</span> <strong style="line-height:1.6">Requirements:</strong> * Hands-on experience with DNA or RNA sequencing...Good underst…

cancer genomic analysis computational biology Job

updated 10.7 years ago • Doe, Aimee

I have some general questions about doing a time series RNA-seq experiment. The RNA is from a non-model organism. The experiment has no conditions for comparison (so just the

DESeq2

updated 3.0 years ago • Dunois

and gRNA screening, and CRISPR genome editing.  We are active contributors to the Bioconductor project. We have developed more than a dozen packages with various utilities, ranging from machine learning, peak calling...software applications as well as providing bioinformatics data analysis support for various research projects. __MAJOR RESPONSIBILITIES:__ * ¥   &…

bioinformatician job Job

updated 8.9 years ago • Julie Zhu