Bioconductor Forum

The Cancer Genomics Research (CGR) laboratory in Gaithersburg, MD, is an advanced, fast-paced, high-throughput organization dedicated to the support of molecular...laboratory investigations of cancer. DCEG/BB is adding computational support, to be provided through CGR, to support methods for large genomic studies including GWAS analysis, somatic mutation analysis, and integrative tumor...We are s…

bioinformatics

updated 2.9 years ago • Wendy

to GRanges ske <- cirs@partitioning # Or PartitioningByEnd(cirs) lens <- lengths(cirs) cgrs <- GRanges( seqnames=rep(seqnames(gal),lens), ranges=unlist(cirs), strand=rep(strand(gal),lens), mcols(gal)[rep(1:length(gal),lens...drop=F]) cgrs <- relist(cgrs,ske) cgrs GRangesList object of length 2: [[1]] GRanges object with 2 range…

GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar

updated 7 months ago • pineiroalejandro

x = "log2_fold_change", y = "adj_p", title = "Edu+ vs EdU- Microglia", xlim = c(-8,10), ylim = c(0,8), selectLab = c(), pCutoff = 0.05, FCcutoff = 0.5849, labSize = 5.…

EnhancedVolcano

updated 4.0 years ago • acharest

site/bcbostoned/ for more information. Questions: email stvjc at channing dot harvard dot edu </div

updated 16.3 years ago • Vincent J. Carey, Jr.

and git. Experience with Bioconductor a plus. Contact stvjc at channing dot harvard dot edu for more details

genetics genomics software Job

updated 5.2 years ago • Vincent J. Carey, Jr.

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

updated 17.2 years ago • Anjan Purkayastha

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

vsn vsn

updated 17.2 years ago • Anjan Purkayastha

with probes attributed to the Hthgu133ahsrefseq - CDF files (http://brainarray.mbni.med.umich .edu/Brainarray/Database/CustomCDF/13.0.0/refseq.asp). On the other hand I'm using CNV-data from agilent (Agilent Human Genome

cdf cdf

updated 15.2 years ago • Noemi Andor

<div class="preformatted">(sending again now that I'm a member of the list) There appears to be a broken link in the "Sources Of Data" section of the Bioconductor web page. The "Unigene Annotation For Affy Chips" link doesn't work. The most obvious error is the lack of ".edu" at the end of the domain name. However, inserting that doesn't restore the link either. Also, how is it decided wh…

Annotation affy Annotation affy

updated 23.6 years ago • Colin A. Smith

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

TimeCourse timecourse TimeCourse timecourse

updated 16.7 years ago • Anjan Purkayastha

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

Normalization Normalization

updated 16.3 years ago • Anjan Purkayastha

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

probe tilingArray probe tilingArray

updated 17.2 years ago • Anjan Purkayastha

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 =========================================== </div

tilingArray tilingArray

updated 17.2 years ago • Anjan Purkayastha

of your best papers and name/contact information of three references to Dr. Wei Li (WL1 at bcm dot edu) with email subject "Postdoctoral application". [[alternative HTML version deleted]] </div

updated 17.1 years ago • Wei Li

due date for applications is _August 21st. _Please send applications to gustin.s AT wehi DOT edu DOT au and put SCHOLARSHIP in the subject line. We hope to see you there

sequencing transcription epigenomics visualization infrastructure News

updated 10.4 years ago • Matthew Ritchie

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

Transcription Normalization probe tilingArray Transcription Normalization probe tilingArray

updated 17.1 years ago • Anjan Purkayastha

<div class="preformatted">Bioconductor basics course in Boston, 24-25 October -- space is limited Tentative agenda --- Oct 24 (Monday) 9am-12pm Vince Carey (VJC, bioconductor core): introduction, software setup, basic programming and structures, annotation 12pm-1pm (lunch on your own) 1pm-4pm Aedin Culhane (Dana Farber Cancer Institute): on clustering/ordination, reproducibility 4pm…

Genetics Cancer Genetics Cancer

updated 14.3 years ago • Vincent J. Carey, Jr.

interests, pdfs of papers, and contact information for three references to peter_park[at]harvard[dot]edu. -- ---------------------------------------------------------------------- Peter J. Park Children's Hospital/Harvard Medical School 77 Avenue Louis Pasteur 255D, Boston, MA 02115 617-525-4468 http

Microarray Microarray

updated 18.9 years ago • Peter J Park

642-5741<br/>email: <a=20 href='3D"mailto:vranizan@uclink.berkeley.edu"'>vranizan@uclink.berkeley. edu= </a=20></div></body></html> ------=_NextPart_000_00DB_01C26305.03E830D0-- </div

rhdf5 affy rhdf5 affy

updated 23.3 years ago • Karen Vranizan

did not happen with earlier version 4.0.x, as I remember. Regards, Hongjian hjnwang [at] cmu [dot] edu

edger edgeR

updated 15 months ago • Hongjian

11 PM, Stephanie M. Gogarten >>> <sdmorris@u.washington.edu <mailto:sdmorris@u.washington.**edu<sdmorris@u.washington.edu="">>> >>> wrote: >>> >>> It's not finding any BAF values that meet all the criteria...Stephanie M. Gogarten >>> <sdmorris@u.washing…

SNP Annotation cdf GWASTools SNP Annotation cdf GWASTools

updated 12.5 years ago • Sam Rose

to Apply__ If you are interested please contact Rachel Myers [rachel(dot)myers(at)duke(dot)edu](mailto:rachel.myers@duke.edu), with subject line CAGPM BioStat III.  Additionally, please apply to the&nbsp

rnaseq precision medicine biomarker genomics Job

updated 7.8 years ago • ram330

the Annual Meeting will be covered by CS. Contact for information and nominations: prinssc (at) jmu (.) edu CS: http://www.classification-society.org/csna [[alternative HTML version deleted]] </div

Classification Classification

updated 17.4 years ago • William Shannon

process, please contact the Principal Investigator directly: yuzun at pennstatehealth psu edu. This is a limited-term non-tenure line position funded for one year from date of hire, with possibility of refunding. Employment

postdoc Computational Bioinformatics Biology Genomics

updated 2.7 years ago • yuzun

General Hospital 149 13th Street, Room 5408 Charlestown, MA 02129 tshtatland at mgh dot harvard dot edu ############################################################ ## read *only* the gcrma-processed dataset (nothing else) into a new R session ## to reduce the number of objects in memory: > load

genefilter PROcess genefilter PROcess

updated 17.8 years ago • Timur Shtatland

General Hospital 149 13th Street, Room 5408 Charlestown, MA 02129 tshtatland at mgh dot harvard dot edu ############################################################ > B <- 1000 > seed <- 99 > TTBoot <- MTP(X=esetGcrmaExprsFiltered, Y=TT, test = "t.twosamp.unequalvar", alternative = "two.sided

multtest multtest

updated 17.9 years ago • Timur Shtatland

General Hospital 149 13th Street, Room 5408 Charlestown, MA 02129 tshtatland at mgh dot harvard dot edu ############################################################ > library(multtest) > nSam <- 5 > X <- matrix(c(1:nSam, 1:nSam+10), nrow=1) > print(X) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 1 2 3 4 5 11 12 13 …

multtest multtest

updated 17.9 years ago • Timur Shtatland

<div class="preformatted"> This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---1903392753-1517917941-1027454075=:15954 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII When I select the "Files" button on the 'MarrayRaw builder' wind…

updated 23.5 years ago • Dick Beyer