it under certain conditions.
Type `license()' or `licence()' for distribution details.
R is a collaborative project with many contributors.
Type `contributors()' for more information.
Type `demo()' for some demos, `help()' for
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I have two datasets
Dataset 1: Control Samples Dataset 2: Case Samples (time-series data - week 1, week 3 and week 8 treatment)
Control and Case individuals are totally different
I would like to analyze...I have two datasets
Dataset 1: Control Samples Dataset 2: Case Samples (time-series data - week 1, week 3 and week 8 treatment)
Control and Case individuals are totally different
…
updated 5.5 years ago • yuvayuvi369
also more efficient?
Also, if I want to cluster these 100M reads based on their
similarity, like editor distance or some distance <=2, is there some
function or package can be used?
Thank you!
Xiaohui
</div
updated 15.1 years ago • Xiaohui Wu
research is becoming increasingly dependent on knowledge stored in computable form. The GO project provides the most comprehensive resource currently available for computable knowledge regarding the functions...with the GO resource
\* encourage exchanges on problems and solutions, and foster collaborations
\* discuss projects with other users as well as with deve…
updated 7.3 years ago • laurent.albou
I have a RNA-Seq time series with two conditions (SD and LD) and 3 time points (0, 2, and 4). There are three biological replicates per sample. I have used
The Institute of Molecular Biology gGmbH
funded by the Boehringer Ingelheim Foundation
is recruiting a
Post-Doctoral Fellow in Bioinformatics Proteome organization and dynamics
(#AKPD02)
The Institute of Molecular Biology (IMB) is a Centre of Excellence for Life Sciences located within the campus of the Johannes Gutenberg University in Mainz, Germany. IMB hosts researchers from a v…
updated 6.2 years ago • l.brown
of experimental and computational genomic research data. The data manager will become the point person for data needs for both dry and wet lab researchers, students and managers.
They will be responsible for the accurate...developed in the lab will be used by world-leading scientists at BC Cancer and international collaborators to gain insight into how cancers initiate, develop and acquire re…
updated 6.6 years ago • jmaanaki
<div class="preformatted">Thank you for your comments. I forward this information to the mailing
list. So others could see it.
Regards,
Peng
On Sun, Aug 9, 2009 at 12:10 AM, <markleeds at="" verizon.net=""> wrote:
> hi: the only way I know of is to install ess+emacs and use that.
that will
> give you? two windows. in one window
> you can have the R code and in t…
updated 16.4 years ago • Peng Yu
class="preformatted">Dear Sir/Madam.
I seek your advice about some microarray data. I have a time serie of
6, from 0, 45m, 90m, 3h 6h and 12h. Each point has 4 replicates. I
want to find diffeentially expressed genes and I am using
updated 15.8 years ago • Helen Zhou
The Thakurela Laboratory in the Department of Pediatrics and Lurie Center for Autism at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) is seeking exceptional candidates in Epigenomics at the postdoctoral level to direct projects involving investigation of neurodevelopment pathways and related neurological disorders.
The Thakurela Laboratory focuses on investigating the eff…
updated 3.2 years ago • sudhir.thakurela
neuropsychiatric gene sets
* Data-driven layer-enriched clustering in the DLPFC
This was a great collaboration between @LieberInstitute @jhubiostat @10xGenomics and in particular by @kr_maynard @lmwebr @sudo_BreeB @mattntran...pmp-a1422614/ @stephaniehicks @martinowk @andrewejaffe
It was a pleasure to be involved in this project!
And if you want to jump in 🤿 and access the data, you can…
updated 5.9 years ago • Leonardo Collado Torres
to the whole genome sequence data of 40,000 cancer genomes from Genomics England’s 100,000 Genome project. Genomics England’s 100,000 Genome project is a large-scale initiative, backed by the UK government, to sequence samples...hunting-for-human-infectious-agents-in-cancer-using-data-from-genomics-england-s-100-000-genome-project
updated 8.9 years ago • Daniel Brewer
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
updated 9.7 years ago • enricoferrero
# Analysis methods for the proteogenomics of oesophageal cancer.
Poster: 04 SEPTEMBER 2017 \[Closing date 1st October\]
We invite enquiries from qualified and highly motivated applicants for a 3 year PhD studentship comprising of tuition fees (Home/EU) and stipend.
__Background__
Oesophageal cancer is a priority area of research. While only the 14th most common cancer in the UK, it is the 6th…
updated 8.3 years ago • Andy Lynch
files that when I open in a
notepad, I see junk. It is in some weird format not
readable in ASCII editors. Also the file size is small
- 4MB.
I saw one my friends converting them to a format
readable by ASCII text. When the conversion
updated 20.9 years ago • S Peri
Full details and application link at <a href="http://www.jobs.cam.ac.uk/job/16356/" target="_blank">http://www.jobs.cam.ac.uk/job/16356/</a>
Application Deadline: __Sunday 8th April 2018__
__Background:__
The MRC Cancer Unit (MRC CU) is a Cambridge University Department situated on the Cambridge Biomedical Campus. It provides an outstanding environment for c…
updated 7.8 years ago • Shamith.Samarajiwa
sequence analysis and motif
extraction, and molecular dynamics.
The position is part of a project on the development of new drugs
against avian flu and other viruses. Toward this end machine learning
and bioinformatics...coiled-coil structure of the avian flu virus surface
protein
hemagglutinin will be investigated. The project is in collaboration
with
the Molecular Libraries and Recognition Gro…
updated 19.7 years ago • Birgit Hauer
Hi all,
I was wondering if there is a package or other tool to track large-scale direction evolution projects. The scope of the tool I'm looking for is a means to track both Sanger and NGS during a directed evolution pipeline, for...all,
I was wondering if there is a package or other tool to track large-scale direction evolution projects. The scope of the tool I'm looking for is a means to trac…
updated 7.7 years ago • JoeMG
<div class="preformatted">Dear bioconductor colleagues
I am fighting with a support project using two colour Agilent arrays.
As
expected with the typical academic microarray study, there are too
many time
points...div class="preformatted">Dear bioconductor colleagues
I am fighting with a support project using two colour Agilent arrays.
As
expected with the typical academic microarray s…
updated 18.9 years ago • Stephen Rudd
Dear all
I am new to microarray analysis and have been assigned a rather challenging project. I'd like to re-analyze published microarray data from GEO. Essentially I would like to do a differential gene expression...Dear all
I am new to microarray analysis and have been assigned a rather challenging project. I'd like to re-analyze published microarray data from GEO. Essentially I would lik…
updated 5.6 years ago • fabian
<div class="preformatted">Hi List,
I apologise for what may be a very simple question. How can I retrieve
the scan date information from cel files?
I can find the information using some editors, kate under linux shows
"a f f y m e t r i x - s c a n - d a t e ( 2 0 0 8 - 0 4 - 0 3"
but I can't find it all all using vi or emacs. I suppose this is
something...How can I retrieve
the scan da…
updated 16.3 years ago • Robert Dunne
min. and two groups (strains)
http://www.bioconductor.org/help/workflows/rnaseqGene/
In the time series chapter it says:
"Genes with small _p_ values from this test are those which, at one or more time points after time 0 showed
updated 4.9 years ago • john
2013; [www.goos.org.uk](http://www.goos.org.uk/)). The team participates in a wide variety of collaborative projects, performing genomic variation analysis, disease mutation discovery, RNA sequence analysis to explore...thinness. You will have excellent communication and organisational skills as you will contribute to collaborative work with colleagues at the Well-come Trust Sanger Insti…
m not joking, and I'm not being snide. This is a manpower issue,
and having worked with open source projects nearly as long as Eric,
can hardly help but agree with him. Documentation, for which we do
better than most, is a huge...spot for this project.
BTW, anyone else who can take a stab at it, feel free to send
criticisms to me, and if relevant or not sure, to the list.
As...describing the …
Hi,
I'm working with time series RNA-seq data, containig 6 time points. There are no replicates and there is no control groupe. I'm interested to find differential
updated 7.5 years ago • bahlv
Hello,
I am new to time-series and multifactorial design. I have read the forum discussions and DESeq2 vignette that deal with multifactorial...Hello,
I am new to time-series and multifactorial design. I have read the forum discussions and DESeq2 vignette that deal with multifactorial designs...on....
I want to clarify if my model or script is not working properly here or that's how …
updated 3.2 years ago • arshad1292
statistical methods/
tools for hypothesis testing and data mining for a range of
biological research projects using up-to-date genomic technologies.
? Consultation and collaborative support to ongoing research
projects. Consulting
updated 20.3 years ago • Diego Diez
The Institute for Biomedicine is home to an international and interdisciplinary team of scientists, students and support staff, integrated in a network of international and national partners. Living and working in Bozen/Bolzano allows you to experience a unique combination of Alpine and Mediterranean culture right at the heart of one of the most exciting mountain regions in Europe.
The Institu…
<div class="preformatted">Dear Gurus,
I am attempting to analyze a bunch of microarray experiments from the
GEO database.
I have experience with Affymetrix chips, so it was reasonably simple
to download the datasets/series of interest, retrieve the relevant
columns from the GSM files (figure out whether they were normalized,
logged, etc), and...I have experience with Affymetrix chips, so i…
updated 16.3 years ago • Ana Rodrigues
Responsibilities Include**
- Lead the interdisciplinary Scientific Computing team in close collaboration with Scionics leadership and the scientific leadership of the client institution, including budget and...planning and management
- Manage the recharging of services provided by the team – including project tracking, time estimates, and project offers
- Work closely with scientists and tea…
updated 5.3 years ago • António Miguel de Jesus Domingues
array preprocessing pipelines?**
Specifically:
* Where do you run your pipeline?
- e.g. Personal PC, local network, HPC using scheduler like SLURM, etc.
* What configuration do you use?
- Nodes, cores, CPU, memory per CPU...or equivalent)
* What kinds of projects do you work on:
- Number of samples, common tasks, significant bottlenecks worth mentioning.
## **Some bac…
updated 3.4 years ago • calen.p.ryan
Hi
I'm finishing a book entitled "R for Bioinformatics" which is part of
the
OReilly bioinformatics series (I have been working f/t on this project
for over a
year, been very quite about it until now....). The book is a
combination of
relevant
updated 22.5 years ago • Kseefeld1@aol.com
**Biostatistics research associate in the University of York, United Kingdom**
Application deadline: 26/05/2021
https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885&p_web_page_id=442112
Applications are invited for a Postdoctoral Research Associate to work on a BBSRC-funded study focussed on uncovering the genetic basis by which plants respond to changes in day le…
updated 4.7 years ago • Daphne
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 21.8 years ago • Enrico Carlon
and played a pivotal role in setting up the Pan-Prostate Cancer Group (http://panprostate.org), a collaboration between all the major prostate cancer sequencing projects in the world.
You will have a graduate level qualification
updated 6.5 years ago • Daniel Brewer
Hi all,
We have an RNA-seq time-series over three time points, measuring the response of a cell line to three treatments (A1, A2 and B). We also have the control
updated 9.2 years ago • Francesca
Hi,
I have a time-series RNA-seq experiment where Drosophila samples are exposed to a certain chemical, call it compound, and subsequently
updated 4 months ago • Denise
an ambitious and motivated individual to contribute to this research. Specifically, the proposed project will focus on analysing large datasets using in-house statistical approaches for joint QTL mapping and network...and *trans* effects. The successful candidate will take a leading role in ongoing interdisciplinary collaborations (involving biologists, clinicians, immunologists and statisticians…
updated 3.8 years ago • helene.ruffieux
Non 1.060912
Mock3 Mock second Not-Infected Non 0.864510
Mock4 Mock third Not-Infected Non 1.064498
L1 L third Not-Infected L 1.137483
... ... ... ... ... ...
V4 Virus third Infected Non 1.104777
LV1 L+Virus first Infected...L 0.862166
LV2 L+Virus first Infected…
updated 14 months ago • JY
**Time-series experiment with patients from 2 conditions and 5 time-points from each patient**
Hi everyone, I am trying to create a DEseq2...Time-series experiment with patients from 2 conditions and 5 time-points from each patient**
Hi everyone, I am trying to create a
updated 4.6 years ago • Karolina Trachtova
<div class="preformatted">Hello edgeR users,
I have been checking around to find out how to best analyze our data
as well as remedy our experiment design. It's hard to decide so I will
try my best to explain what we have, what we want in a rather long
message. Please bear with me.
FIRSTLY SOME WORDS ABOUT OUR SAMPLES:
We did experiments with two groups of test animals namely treated "T"
a…
updated 11.4 years ago • Vang Le
Tremendous opportunities for discovery are emerging in the biological and biomedical sciences, as well as in traditional physical and social sciences, but they will require the combined power of theory, data analysis, and simulation. In the biomedical sciences, for example, researchers are being confronted by an explosion of information from genome sequencing, gene expression profiling, proteomic…
updated 4.3 years ago • simonsF.careers
Hat Enterprise Linux Server release 6.9 (Santiago)
Matrix products: default
BLAS: /GWD/bioinfo/projects/cb-software/personal/ef884766/lib64/R/lib/libRblas.so
LAPACK: /GWD/bioinfo/projects/cb-software/personal/ef884766
updated 8.7 years ago • enricoferrero
The focus of the Section of [Computational Biomedicine](https://www.bumc.bu.edu/compbiomed/) at Boston University School of Medicine (BUSM) is to develop and apply computational methods for high-throughput genomic technologies to understand and characterize a variety of biological systems and diseases. Several labs within the section collaborate and have joint research interests in the lung to u…
updated 4.4 years ago • camp
PI regularly and contribute to the success of the research team.
- Develop and maintain productive collaborations within Mount Sinai and with outside researchers in academia and industry.
- Publish and present novel research...to deadlines.
- Excellent oral and written communication skills with track record of productive collaborations.
- Demonstrated ability to work concurrently on sever…
updated 6.2 years ago • supindab
would be advantageous.
The above post will involve working closely with laboratory staff and
collaboration with other bioinformaticians so you are expected to have
good
communication skills.
Senior Bioinformatics...for the Bioinformatics and
BioStatistics
Service support of array-based SNP and genotyping projects across
Cancer
Research UK.
You should have a higher degree in bioinformatics, sta…
updated 20.3 years ago • Gavin Kelly
I want to project the identified tophits genes(RNA-Seq) and proteins(proteomics MS/MS) onto a network of protein-protein interaction
updated 9.6 years ago • Abhishek Pratap
facilities of
the Roy J. Carver Biotechnology Center. This includes support of all
on-going projects of the Biotechnology Center in genome sequencing,
and comparative and functional genomics. These projects may...of data analysis workflows, quality
control, data tracking and reporting procedures, in close
collaboration with the Director of the facility. Supervise and train
academic and technical …
updated 13.8 years ago • Jenny Drnevich
There are a series of amino acid sequences I want to import into R for alignment ,using DECIPHER, with some sequences I imported as FASTA...processed trimmed versions of the ".prp" files.
When I simply open the files using my native text editor they are not fast format which I have worked with before, they look like this:
___emm1.0___
___M1 type-specific region
updated 8.0 years ago • reubenmcgregor88
su www.sienabiotech.com? .
The Company, Siena Biotech SpA, as data??controller, deals with your
personal data only for administrative and??accounting purposes of its
activities, even in case of the communication??to third
I just quickly check the data from TCGA project and found that some number of reads are greater than the target library size 40 million. Any ideas? Similarly for GTEx
updated 6.7 years ago • Sheldon Pang
to understand and discover regulatory rules in pro and anti carcinogenic processes.
__The project:__
Supervised by Dr. Shamith Samarajiwa at the MRC cancer unit (A department within the clinical school, University...processes that can be targeted for designing anti-cancer therapeutics. This multidisciplinary project will provide the ideal candidate with the required quantitative skills an excit…
updated 8.2 years ago • Shamith.Samarajiwa
<div class="preformatted">
Hi to all,
After I tried with several text editors, in several different PC and
laptops, the problem persist. I talked with another guy in Rome who
has the
same problem, and he is the only BioC-WinXP user I know...
With windowsXP, once I installed and LOADED samr or pamr packages, all
the
error messages appear in a pop-up window. This doesn't happen with all
the…
This position requires the ability to work independently, manage multiple overlapping data analysis projects, and communicate effectively with faculty, post-doctoral fellows, and research staff on a wide range of topics in...designs
- Identify best-practice bioinformatics tools and strategies to meet the needs of proposed projects
- Provide figures and written sections describing methods and re…
updated 2.5 years ago • Chao-Jen Wong
questions in epigenetics, gene regulation, RNA biology and genome stability. Recent exemplary project include comparison of transcriptome and proteome data (Dejung et al., PLOS Pathog 2016), large- scale temporal proteome...e.g. GSEA, comparison to published datasets)
*
Support lab members and collaborators with your bioinformatics skills
__Requ…
updated 8.1 years ago • Mario Dejung
would
like to receive your expert opinion on this.
The platform is cDNA array with two experimental series.
- On series 1 chips, tumor sample from a patient (Cy5) and normal
sample from pooled healthy individuals (Cy3) were co-hybridized...On series 2 chips, cirrhosis sample from that patient (Cy5) and and
normal sample from pooled healthy individuals (Cy3) were co...analysis.
The request that …
updated 17.2 years ago • Seungwoo Hwang
I should specify that this is on a large compute cluster. I install all my packages in a personal library, to which I point with .libPaths(). I am facing no such issue with over 100 other packages.
Thanks for any advice...this problem.
Alex
```r
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
> .libPaths("/project/6026769/R/x86_64-pc-linux-gnu-library/4.3.1")
> li…
updated 24 months ago • alexandre.blais
RNA seq analysis but it seems the processing is taking longer than what I have been able to do on my personal computer. Please let me know if there is anything else I need to send.
<pre>
$ screen -S DESeq2
### DESeq2 Analysis in Server...setwd('/projects/home/cyoung304/data')
library('DESeq2')
cts <- read.csv(file='GeneName.csv')
nrow(cts)
ncol(cts)
co…
updated 7.0 years ago • coyoung
Postdoctoral Researcher in statistical analyses and modelling of drug combination data (ERC funding)
and safe cancer treatments for personalized medicine.
The open position is part of the __ERC funded project __[DrugComb](http://cordis.europa.eu/project/rcn/210127_en.html) in the field of computational drug combination...and experience:__ The postdoctoral researcher will be jointly responsible for driving the projects and supervising PhD students in an interdisciplinary and collaborat…
updated 8.2 years ago • jing.tang
Tremendous opportunities for discovery are emerging in the biological and biomedical sciences, as well as in traditional physical and social sciences, but they will require the combined power of theory, data analysis, and simulation. In the biomedical sciences, for example, researchers are being confronted by an explosion of information from genome sequencing, gene expression profiling, proteomic…
updated 4.0 years ago • simonsF.careers
Recent ...
Replies
Comment: Converting Probe IDs to HGNC symbols
by
nana
•
0
Converting probe IDs to HGNC gene symbols depends on the platform the probes come from (Affymetrix, Illumina, Agilent, etc.). Below are the…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴
10
Thank you @seandavi for your feedback.
I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★
4.1k
Hope you don't mind I am not Johannes... ;-)
Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
•
0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
•
0
Dear Johannes,
Would it be possible to generate a EnsDb for the newest Medicago V5 genome release?
Medicago truncatula A17 r5.0
This woul…
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