<div class="preformatted">
Marc,
Thank you very much for the information. Does it mean that I have to
use those acceptable "evidence code" to GOstats package or I can have
my personal label?
Thanks.
X.G.
Date: Tue, 22 Jan 2013 10:23:45 -0800
From: Marc Carlson <mcarlson@fhcrc.org>
To: bioconductor@r-project.org
Subject: Re: [BioC] question about "evidence code" in data.frame from…
Order by: Relevance
in the computational analysis of NGS and other “omics” data generated in the course of research projects. We are looking for a highly motivated Bioinformatician (m/f/d) to join our Core Facility team and establish a platform...Knowledge of software engineering and bioinformatics pipelines
- Experience in interdisciplinary collaborations or bioinformatics services
**We offer:**
- Stimulat…
updated 5.4 years ago • sergisayolspuig
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 14.2 years ago • Ivan Gregoretti
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 10.2 years ago • virctoalgn
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 5.3 years ago • guoyinping
reporting to the Global Head, Exploratory Statistics, and embedded/co-located with the scientific collaborators. This position can be based in Worcester, MA or in North Chicago, IL.</p>
<h2>Key Responsibilities:</h2>
<ul>
<li>Help build...with discovery and clinical scientists, statisticians, computational biologists, and external collaborators to drive program decis…
updated 10.9 years ago • Feng Hong
We seek a talented and highly motivated data analyst to join our exciting project applying artificial intelligence methods to understand immune and inflammatory (including immunotherapy) responses...in cancer. The project will be based at the Systems Biomedicine lab https://www.samarajiwa-lab.org, MRC Cancer Unit, University of Cambridge...learning to multi-omic datasets in order to understand an…
updated 6.2 years ago • Shamith.Samarajiwa
Hi
When i want to use getGEO function to download GSE dataset with this code:
series <- "GSE85358"
gset <- getGEO(series , GSEMatrix =TRUE, AnnotGPL=TRUE, destdir = "....." )
,i encounter this error:
https://ftp.ncbi.nlm.nih.gov...Hi
When i want to use getGEO function to download GSE dataset with this code:
series <- "GSE85358"
gset <- g…
updated 7.4 years ago • maryam.sabet
to an open and inclusive research environment;
- good written and oral communication skills.
The project is funded by the Fonds National de la Recherche Scientifique (FNRS). The position is open immediately until filled...working hours and the possibility to work remotely. The lab meetings are typically scheduled in-person (or mixed remote/in-person) to favour interactions among lab members. …
updated 2.8 years ago • Laurent Gatto
asked back in 2010 (
http://article.gmane.org/gmane.comp.lang.r.sequencing/1663/match=edgeR
+time+serie
)
I have an RNA Seq experiment with 2 replicates of 8 time points with
both a
control and treatment conditions. Time point
updated 13.0 years ago • Marcelo
I have 8 samples that correspond to 4 persons measured in two times, 0h and 20h.
- names_chip person time sample
- 1 IonCode_0109 A1 0 Donor 1- Day 0
- 2 IonCode_0110 A1 20...dds <- DESeqDataSetFromMatrix(countData = counts,
colData = annotation,
design = ~ time+person)
I have made pca plots and clustering of normalizated counts and i can see that the samples of the …
updated 6.8 years ago • acebolladaso.iacs
Overview: This highly collaborative position provides a unique opportunity for multi-disciplinary research spanning Systems Immunology...Perform cytometry data annotation, curation, and harmonization as needed.
- Work independently and collaboratively with Long lab and HIP Core researchers to design, implement, and analyze new
immunological experiments...implement best-of-class methods (i) …
updated 4.1 years ago • hbolouri
49-30-450 569124
peter.robinson@charite.de
http://www.charite.de/ch/medgen/robinson
The best editor for MS Word documents: /dev/null</div
updated 20.9 years ago • Robinson, Peter
Dear Heidi good morning !
We made some more work on HTqPCR (actually, mainly Elena..) and we
have
an update
and a question for you:
=> update: seemingly with the latest HTqPCR it is not possible to
import
anymore
datasets in a simple format, gene name, Ct, group for example, with
readCtData().
Did you receive any observation from other groups on this ?
=> data normalization: now normali…
updated 12.2 years ago • alessandro.guffanti@genomnia.com
Hi everybody,
I have a question regarding comparing results from a t-test and limma.
I compared the p values obtained from both algorithms using 100
samples in each condition. Given the large number of observations my
expectation was to see high correlation between the p values. As shown
below, I ran the same code in three different conditions for the mean
and standard deviation. The mean and st…
updated 11.6 years ago • Guest User
Hi everybody,
I have a question regarding comparing limma and the t-test. I compared
the
p values obtained from both algorithms using 100 samples in each
condition.
Given the large number of observations my expectation was to see high
correlation between the p values. As shown below, I ran the same code
in
three different conditions for the mean and standard deviation. The
mean
and standard devi…
updated 11.6 years ago • Giovanni Bucci
of Muenster.
The position will involve interacting mostly with the Stoll group but
also with collaborators at the Max Delbrueck Center for Molecular
Medicine (MDC) in Berlin-Buch, the Broad Institute of MIT and Harvard...the in house Illumina Core facility (microarray data, next generation
sequencing data). The initial project is flexible, depending on the
candidate, but it must contribute to the…
analyzing metabolomic data, so I have no specific
recommendations to make. I suggest you to collaborate with a
statistician to try to find the best normalization method for your
specific data. again, if you like, you...on PLGEM and actually used a bit
Of it in my former spectral count based quantitative proteomics
project back in Suizzera.
Now I found myself quite close to you dealing with a bit…
updated 13.3 years ago • Norman Pavelka
### 100% Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks
## 2-2.5 year fixed-term contract available immediately or as agreed
Understanding how a fertilized egg develops into a complex multicellular organism is one of the most fascinating topics in biology. The current challenge is to understand how genes function as part of gene regulatory networks (GRNs) that contr…
updated 4.1 years ago • Robert Ivanek
from the same
procedures!
But, the first and second gene expression data are identical, the
third gene
expression data are different with the other two.
Why the third data expression is different? How I can progress
updated 18.4 years ago • Meiyin.Gao@unibas.ch
<div class="preformatted">Dear Sean and James,
first of all, I would like to apologize for my late reply. There were
a lot of storms yesterday here at Oviedo, and a lot of derived
technical problems at my workplace which kept me from accessing the
net.
Thank you for your kind replies. Having read James' answer, I tried to
replicate again the problematic commands:
> gpl <- g…
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
and molecular laboratories from
Harvard Medical School, Channing Laboratory, and External
Collaborators perform the following:
??? Develop and manage development of the specification documents for
database tables...against schedules to management as appropriate;
??? Generate Reports for Principle Investigator or Project Manager; To
ensure completion of assignments within established timelines.
…
pa inc
The Cambridge Research Institute (CRI) is a major new initiative of
Cancer
Research UK, in collaboration with the University of Cambridge.
Strategically situated on the Addenbrooke's biomedical campus, the
Institute...to join our growing team and support
microarray and next generation sequencing based projects. You will
work
closely with scientists on a regular basis analyzing data genera…
updated 16.5 years ago • Mark Dunning
The Hughey Lab in the Department of Biomedical Informatics at Vanderbilt is looking for exceptional individuals to join the team. We're interested in people who are hard-working, creative, and eager to learn. Successful applicants will have the opportunity to shape the research directions and culture of the lab. The lab is recruiting at all levels. NIH-funded positions are available to start imme…
updated 7.9 years ago • Jake
Fwd: Re: Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
<div class="preformatted">Hello,
without touching upon any recent changes in biocLite, I would
recommend
the following simple way to install packages without administrator
rights.
1. Create an environment variable called "R_LIBS" and point that a
writeable directory where you want your packages to go to. For example
in the ~/.bashrc set something like:
export R_LIBS="${HOME}/rpackages"
Sy…
keep it constant between different files (at least if this is not
something totally stupid to try).
Third, I have created densityplots and noticed that the order of files
is not like the order in the phenoData info. In phenoData...Po-Box 1105 Blindern
N-0317 Oslo
Domus Medica
Room 2362
Tel: +47-22851137
http://www.uio.no/sok?person=anjasc
</div
seek a talented and highly motivated computational biologist or bioinformatician to join an exciting project applying computational biology to understand gene and epigenome regulation in cancer. The project will be based...in order to understand gene and epigenome regulation in processes influencing cancer formation. The project will utilize datasets generated by our experimental collaborators as…
updated 5.9 years ago • Shamith.Samarajiwa
data, analysis plan, and timelines. As part of a larger team of statisticians, programmers, and project managers, the SRA also contributes to an environment of mutual cooperation and respect. The SRA handles multiple...projects and works efficiently in a fast-paced environment.
### Responsibilities
Under limited technical direction, the SRA...Perform exploratory visualization and analyses
* P…
updated 7.7 years ago • Fred Hutch (Recruiting)
I was wondering if it was possible to annotate my DESeq2 genes with my tx2gene file by having a third column with gene names/ids
updated 5.6 years ago • pthom010
Hello,
My recent RNA-Seq experiment had a few samples with high counts of rRNA genes in the third replicate. My pipeline was HISAT2 --> featureCounts --> DESeq2.
When clustering replicates 1 and 2, the replicates of...Hello,
My recent RNA-Seq experiment had a few samples with high counts of rRNA genes in the third replicate. My pipeline was HISAT2 --> featureCounts --&am…
updated 4.2 years ago • jac
fibroblast </span>
<span style="background-color:rgb(245, 245, 255)">Sample3: (Control person \#1) blood</span>
<span style="background-color:rgb(245, 245, 255)">Sample4: (Control person \#1) fibroblast </span>
<span style="background...color:rgb(245, 245, 255)">Sample5: (Control person \#2) blood</span>
<span style="backgroun…
facilitating the acceleration of technology development. The group also fosters significant collaborations with clinicians, other academics and selected industrial partners.
Our research focuses on the chemical...publications>).
The post-holder will work as a bioinformatics analyst contributing to several projects such as:
* Elucidating the fundamental role of non-cano…
updated 9.2 years ago • sergio.martinezcuesta
Aid research laboratories in designing interpretable sequencing
experiments and studies
- Collaborate with primary investigators and other scientists to
analyze data in both exploratory and hypothesis driven...meetings
- Co-author peer-reviewed scientific manuscripts
- Maintain thorough records for each project and ensure data are
reliably backed-up
**You will need:**
- A…
updated 4.6 years ago • rbrns
<div class="preformatted">We are looking for a talented and enthusiastic bioinformatician to
join the Bioinformatics Core at the prestigious Cancer Research UK
Cambridge Institute.
For informal enquiries please contact Suraj Menon (suraj.menon at
cruk.cam.ac.uk)
http://www.jobs.cam.ac.uk/job/4756/
Bioinformatics Analyst
Located at the heart of the Addenbrookes Biomedical Campus, the Can…
updated 11.4 years ago • Suraj Menon
I am looking for **Data Engineer** who would like to join our NaturalAntibody team to work on its computational antibody drug discovery product portfolio.
****About the role****
As a **Senior Data Engineer** you will design and work on our data and analytics stacks. You will contribute to our data stack by analysing our existing databases and creating novel datasets. You will employ this …
statistical and computational methods
for processing and interpreting genome-scale datasets in close
collaboration with biologists, and spans basic science and clinical
applications.
For further information, see <http: mrobin...throughput genomic technologies (e.g. massively parallel sequencing,
microarrays). Several exciting projects are now underway, including
but not limited to methods fo…
updated 13.2 years ago • Mark Robinson
like crazy after two news releases this
week. Huge expansion plus multi-million dollar development projects
are
pushing share prices through the roof. Act fast and get on SZSN first
thing Monday!
I have simpler code that focuses...historical moment.
Defining a strong modular architecture enables a disparate set of
developers to collaborate on producing a compliant Java technology
implementation.…
updated 18.5 years ago • Theodore
I would like to identify the cell line-independent differentially expressed genes in a time series experiment, i.e. those genes that respond similarly to the stimulus regardless of cell line background. This is the
updated 6.4 years ago • jhnwphillips
for EMBL researchers
• Teaching short courses on computational statistics / data science in biology
• Collaboration on selected research projects with EMBL research groups
As statistician/data scientist, you will be interested...care facility on campus. EMBL has a large thriving community of bioinformaticians, working in close collaboration with experimental scientists and with strong links …
a relation between the expression of any genes and X (a continuous variable). For my design I have 5 persons and samples where taken from those at 3 different times. I think the design would be:
~ Persons + time + X
Is this correct?
Thank
updated 9.2 years ago • sasha
and late stage development of products at Roche. DevSci supports drug discovery and development projects across all therapeutic areas from discovery to launch (and beyond). We are poised at a unique time when large volumes...This role will be responsible for contributing to and helping drive data lifecycle management projects that enable the storage, organization, dissemination, and analytics of …
updated 3.9 years ago • nwalton
<div class="preformatted">Hi all,
Allow me to add my perspective as a relative newcomer into this field.
At first I too was alarmed by the apparent violation of statistical
orthodoxy involved in pre-filtering. But after witnessing how well
this works on real data, my opinion has changed.
I feel that either the statistician's perspective of p-values and
inference or the data-miner's persp…
updated 17.5 years ago • Assaf Oron
First I mapped their GenBank probe IDs into UniGene IDs. By doing so,
it turned out that array series A has ~11,000 unique UniGene probe
IDs, array series B has ~10,000 unique UniGene probe IDs, and their
intersection is ~6,000...Thus, after normalizing array series A and B
separately, I have the following data;
Array A series
ID replicate1 replicate2 ... replicateN
A1 logRatioA1.1 logRatio…
updated 17.4 years ago • Seungwoo Hwang
nbsp;GiHub issue (issue no. 395) , and someone assigned to look at my package. I have contacted that person for the same problem but that person never replies the comment. Is there any way to speed up the process
updated 8.6 years ago • Mohamad S. Hasan
data analysis. The candidate will be working closely with the team on a number of cancer proteomics projects funded by NCI/NIH. More details about cancer proteomics projects can be found [here](https://proteomics.cancer.gov...Some of the downstream efforts will include integration of proteomics data with transcriptomics and personal genomics or so-called proteogenomics. The candidate will learn a…
updated 8.0 years ago • petyuk
The Institute of Molecular Biology gGmbH
funded by the Boehringer Ingelheim Foundation
2 Postdoc Positions available
1 Computational Biologist and 1 Molecular Biologist
non-coding RNA & R-loop epigenetics
The Institute of Molecular Biology gGmbH (IMB) is a Centre of Excellence for Life Sciences, funded by the Boehringer Ingelheim Foundation. It is located within…
updated 7.2 years ago • l.brown
is only the timepoints? I would love to have some input from someone with experience analyzing time series RNA-seq data where measurements were taken for each individual at each time points were taken. Thank you in advance
updated 2.7 years ago • Hongru
factorization that have underpinned our recent Nature Genetics and Nature publications. First, the project will involve investigating the relationship between clonal cell expansions in morphologically normal tissue...and the presence of prostate cancer in an expanded series of prostates both from patients with prostate cancer and those without. This will allow us to determine the prevalence
we finally decided to separate genotypes and local/systemic responses, so the final design is a time-series experiment with 4 sampling times (6 h, 24 h, 72 h and 144 h after infection) and two conditions, control and treated plants
updated 5.7 years ago • Victor Chano
Fully-funded Ph.D. scholarship within evolutionary/functional genomics in Norway**
The project aims to understand the phenotypic/adaptive/gene regulation effects of structural variants by using statistical...functional genomics analysis (For example, DeSeq2, Kallisto, STAR)
**You need to:**
Have good collaborative skills and high motivation. You will closely work with another PhD studen…
updated 4.5 years ago • marie
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 18.3 years ago • Groot, Philip de
I am trying to process GEO series, like GSE36411 data (Illumina data) using lumi package and limma package.
I am getting following following error for...above mentioned series and for many such series.
> raw.data <- read.ilmn(files="GSE36411\_non-normalized.txt")
Reading file GSE36411\_non
updated 7.6 years ago • hks04180
Hello,
I have a question regarding the results output of the Wald test I'm running in DESeq2. I have time-series data with samples collected at 5 time points b/w 2 genotypes: 0hr, 2hr, 6hr, 12hr, 24hr and mutant vs. control. My question is...I have a question regarding the results output of the Wald test I'm running in DESeq2. I have time-series data with samples collected at 5 time points b/w …
updated 4.3 years ago • jd348
active materials.
FRF positions are initially two-year appointments, renewable for a third year contingent upon performance. Flatiron Research Fellows will report to research scientists, group leaders, or...process large amounts of data
• Ability to work well in an interdisciplinary environment, and to collaborate with experimentalists
• Strong oral and written communication, data document…
updated 4.0 years ago • simonsF.careers
by gathering the top 20 genes with the lowest padj values in the `results` from the whole time series. That is, these are the genes that at one or more time points showed differences between the two strains tests.
- However
updated 6.8 years ago • courtney.stairs
Dear all,
I have a time series RNA-seq experiment with a control at time 0 and would like to test the inhibitors effect over time (4h, 24h) but also want
updated 9.2 years ago • aec
<div class="preformatted">Dear all,
We have a number of research and programming positions available in
Computational biology and Bioinformatics:
The Paterson Institute for Cancer Research in Manchester is a leading
cancer
centre of excellence core-funded by Cancer Research UK, the largest
independent cancer research organisation in the world. The Institute
supports numerous basic and tra…
updated 17.2 years ago • Crispin Miller
and integrate heterogeneous high-dimensional data as found in multi-omics biomedical research projects, especially in cancer studies. In close collaboration with biologists and clinicians, we will adapt approaches...in a relevant subject is required.
__We offer__ a productive, interdisciplinary and extremely collaborative work environment, excellent technical facilities, strong ties to clinical …
updated 10.5 years ago • Simon Anders
[Click to Apply at St Jude Website:][1] and better send CV to beisi.xu[at]stjude.org
**Overview**
[The Epigenetics Group from the Center for Applied Bioinformatics][2] at St. Jude Children's Research Hospital is looking for a highly motivated and creative Bioinformatics Research Scientist or Lead Bioinformatics Analyst to develop and apply innovative analytical approaches to understand the und…
updated 3.6 years ago • xubeisi
Recent ...
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