Bioconductor Forum

_Unique.count.table <- easyRNASeq( filesDirectory = "./FruMA\_Male\_WCS\_Male/tophat\_BAM\_files/", organism = "Dmelanogaster", readLength=100L, chr.sizes = "auto", annotationMethod = "gtf", annotationFile = "Drosophila\_melanogaster.BDGP5.77.gtf...FruMA\_Male\_WCS\_Male/tophat\_BAM\_files/",        organism = "Dmelanogaster", readLe…

easyRNASeq

updated 10.7 years ago • surjray

NULL for (tcga_ind in seq(nrow(tcga_proj))) { proj_info <- tcga_proj[tcga_ind, c("project", "organism", "project_home")] rse_gene_temp<- create_rse(proj_info) count_matrix <- rse_gene_temp@assays@data$raw_counts

recount3 TCGA RNASeq

updated 2.3 years ago • tangming2005

signal transduction in cancer, genetics and development, including human genetics, stem cells and organ development, infection and inflammation and metabolism and hormones. The de Duve Institute also features several

pRoloc proteomics Spatial Proteomics MassSpectrometry

updated 3.0 years ago • Laurent Gatto

<div class="preformatted">Mark Robinson <mrobinson at="" wehi.edu.au=""> writes: > Hi An. > >> With respect to xps, your reference to script4xps.R is really >> helpful. Do you have a URL from where the files "MoEx-1_0-st- >> v1.r2.clf", "MoEx-1_0-st-v1.r2.pgf", "MoEx-1_0-st- >> v1.na25.mm9.probeset.csv", "MoEx-1_0…

Epigenetics Cancer probe affy xps Epigenetics Cancer probe affy xps

updated 17.6 years ago • Martin Morgan

<div class="preformatted">Dear all, Simon Anders kindly asked me to repeat my question on this mailing list considering the statistical analysis of my RNA sequencing data. I am rather new to Bioconductor and RNA sequencing analysis (molecular biologist) and tried to read myself a bit into the statistics behind the analysis in DESeq and found the publication of "Storey & Tibshirani…

Sequencing Organism qvalue DESeq Sequencing Organism qvalue DESeq

updated 14.3 years ago • Markus Grohme

package: GenomicFeatures # Data source: /Users/Mmul_8.0.1/Macaca_mulatta.Mmul_8.0.1.97.chr.gtf # Organism: NA # Taxonomy ID: NA # miRBase build ID: NA # Genome: NA # Nb of transcripts: 55075 # Db created by: GenomicFeatures package from

TxDb GenomicFeatures

updated 5.6 years ago • Brian Smith

from the AnnotationDbi package version 1.18.1 (under R 2.15.1 / Bioconductor 2.10) for the organism 'Oryctolagus cuniculus' (Rabbit - NCBI taxonomy id 9986). Please, see transcript below for the details. Can anyone assist

GO AnnotationDbi GO AnnotationDbi

updated 13.5 years ago • Osselaer, Steven [JRDBE Extern]

SWITCHTOI: Contact Us > > FirstName: Lynn > LastName: Amon > Title: Staff Scientist > Organization: Fred Hutchinson Cancer Research Center > Email: lamon at fhcrc.org > Phone: 206-667-7836 > Comments: Why are

Annotation Cancer bgx Annotation Cancer bgx

updated 17.8 years ago • Lynn Amon

Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end [goid 8150] [evidence ND...Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with …

Network Homo sapiens limma PROcess Network Homo sapiens limma PROcess

updated 13.5 years ago • Seyed Ahmad Mousavi

Code should be placed in three backticks as shown below ```r my_gtf_1 <- makeTxDbFromEnsembl(organism="Homo sapiens", release=86, circ_seqs=NULL, server="ensembldb.ensembl.org", username="anonymous", password=NULL, port

DEXSeq dex

updated 3.3 years ago • barrypraveen

In addition to individualized strategies, physiotherapists in Abbotsford work with sports teams and organizations to implement injury prevention protocols. These may include team-wide warm-up routines, cool-down sessions

omada NestLink

updated 2.2 years ago • physiotherapytownline

<div class="preformatted"> >Hmm, your answer left me thinking about how to measure distances. Why >doesnt a distace function just calculate the distance between the values >that are there and leave out the NA:s? I have filtered away with the >B-test the spots that are supposedly not to be differentially expressed >and have only a subset of the total number…

updated 22.3 years ago • Marcus

from embryo to mature adult. Each stage has been sampled at uneven timepoints according to the organism development scheme (e.g.: every 2hrs for the embryo, at every larval stage for the larvae). For each timepoints I have

drosophila melanogaster multiple time points deseq2 results development

updated 9.0 years ago • wariobrega

chromlen, dataSource="gff3 file of haustorial effectors from 12SD80", organism="Puccinia coronata")</pre> [https://s3.msi.umn.edu/txdb\_troubleshooting/haus\_expr\_secreted\_effectors\_sd80\_p.full.gff3

genomicfeatures txdb maketxdbfromgff

updated 7.6 years ago • marisa.e.miller

Hi I'm getting some warnings in > makeTxDbFromGFF() here is full stacktrace: ``` Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: /home/weir/RNAedit/human_test/reference/GCF_000001405.38_GRCh38.p12_genomic.gf…

txdb

updated 4.9 years ago • weir

dat[2,] + 2*rep(1:3,each=3) # another true positive groups <- gl(3,3,labels=letters[1:3]) # organize the data in 3 groups # basic testing in limma (emprical Bayes) require(limma) (design1 <- model.matrix( ~ -1 + groups )) (contr.matr1

limma limma

updated 16.4 years ago • Wolfgang RAFFELSBERGER

lumiHumanAll.db' ,ont = "MF", pvalueCutoff = 0.01, readable = TRUE) z = enrichKEGG(gene = list, organism = "hsa", pvalueCutoff = 0.05) plot(x) plot(y) plot(z)   sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86\_64-apple-darwin13.4.0

clusterprofiler

updated 9.5 years ago • joseph

for RRBS (NCBI version GRCh38.p11) Description: Homo Sapiens full genome as provided by NCBI organism: Homo sapiens common\_name: Human provider: NCBI provider\_version: GRCh38.p11 release\_date: 14/06/17 release\_name...source\_url: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF\_000001405.37\_GRCh38.p11/ organism\_biocview: Homo\_sapiens BSgenomeObjname: H…

bsgenome forge TwoBits_export

updated 8.4 years ago • stu111538

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

PostDoc JobPosting Basel Switzerland

updated 4.2 years ago • Robert Ivanek

signal transduction in cancer, genetics and development, including human genetics, stem cells and organ development, infection and inflammation and metabolism and hormones. The de Duve Institute also features several

Proteomics SingleCell JobPosting MassSpectrometry

updated 3.0 years ago • Laurent Gatto

<div class="preformatted">On Mon, Jun 2, 2008 at 5:03 AM, Eleni Christodoulou <elenichri at="" gmail.com=""> wrote: > Thank you guys, > > I saw your answers this morning. I downloaded the package "org.Hs.eg.db", > but I am struggling a bit with the use of the commands. I am trying for > example: > x <- mget("AA868688",org.Hs.egACCNUM2EG…

Annotation GO convert biomaRt Annotation GO convert biomaRt

updated 17.8 years ago • Sean Davis

Term Ont N Up Down P.Up P.Down GO:0043252 sodium-independent organic anion transport BP 2 2 0 6.017011e-05 1 GO:0006270 DNA replication initiation BP 8 2 0 1.635777e-03 1 GO:0071881 adenylate

limma goana edger

updated 7.6 years ago • b.nota

change the default for circ_seqs in makeTranscriptDbFromBiomart to be NULL, instead of any organism (human) specific. Regards, --Malcolm R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale

TranscriptDb biomaRt GenomicFeatures TranscriptDb biomaRt GenomicFeatures

updated 14.1 years ago • Malcolm Cook

Additional Information about this package: DB schema: MOUSECHIP_DB DB schema version: 2.1 Organism: Mus musculus Date for NCBI data: 2015-Mar17 Date for GO data: 20150314 Date for KEGG data: 2011-Mar15 Date for Golden

annotation annotationdata illuminaMousev1p1.db

updated 9.1 years ago • Guido Hooiveld

analysis on high-throughput genome-wide datasets in a wide range of research projects and different organisms. The bioinformatician will work in a highly collaborative environment, carry out data analysis and integration

next-generation sequencing rna-seq chip-seq single cell Job

updated 9.8 years ago • Katja Hebestreit

keys) Additional Information about this package: DB schema: MOUSECHIP_DB DB schema version: 1.0 Organism: Mus musculus Date for NCBI data: 2008-Apr2 Date for GO data: 200803 Date for KEGG data: 2008-Apr1 Date for Golden Path

GO ChipName AnnBuilder AnnotationDbi GO ChipName AnnBuilder AnnotationDbi

updated 17.4 years ago • swang

<div class="preformatted">Paul Shannon <pshannon ...="" at=""> writes: > > I offer below a short example of using rGADEM with MotifDb which you may find useful. > > The example motivates and then demonstrates "seeded" search, in which a candidate TF is provided to > rGADEM. (The rGADEM vignette illustrates the simpler task of de novo motif search. …

rGADEM MotIV MotifDb rGADEM MotIV MotifDb

updated 12.0 years ago • Bahar

All you need is an annotation column that you can map to gene symbols, then use the Bioconductor organism package for your species (eg org.Hs.eg.db) to map from symbols to GO terms. limma will probably read in annotation

Microarray Annotation GO Organism limma GOstats oligo ASSIGN Microarray Annotation GO

updated 14.2 years ago • Gordon Smyth

<div class="preformatted">Hi and thank you for your answer Dr. Carvalho, I read the NDF manually. There are numbers from 1 to 461 in the PROBE_CLASS column. Is the solution to change the numbers into word "experimental"? Thank you, Zeynep 2012/4/24 Benilton Carvalho <beniltoncarvalho@gmail.com> > If you read the NDF manually, what are the values for the column > PR…

BiocViews Annotation Organism biocViews pdInfoBuilder charm BiocViews BiocViews Annotation

updated 13.9 years ago • zeynep özkeserli

I would like to create a data.frame with both ENSEMBL and ENTREZID gene identifiers for several species, including the human and the *Macaca fascicularis* genomes. I noticed that the latest EnsDb object available (`AH100643` = ensemble version 106) for the human genome only contains ENTREZIDs for ~ 40% of the ENSEMBL gene identifiers. (See reproducible example below.) In contrast, the `org.Hs.e…

AnnotationHub org.Hs.eg.db ensembldb

updated 3.6 years ago • sandmann.t

<div class="preformatted">(We apologize for multiples copies) (Please distribute) ---------------------------------------------------------------------- ----- 1st Call for Papers - 2nd International Symposium on Distributed Computing and Artificial Intelligence (DCAI'09) June 10th â 12th , 2009 - Salamanca - Spain http://dcai.usal.es/ The International Symposium on Distributed Computing…

updated 17.2 years ago • Nora Muda

Gabor Csardi <gabor.csardi@foo.bar>", Maintainer = "Gabor Csardi <gabor.csardi@foo.bar>", organism = "Homo sapiens", species = "Human", biocViews = "AnnotationData, FunctionalAnnotation", DBschema = "TARGETSCAN_DB", AnnObjTarget

BiocViews miRNA Annotation Cancer Organism biocViews AnnotationDbi BiocViews BiocViews

updated 13.7 years ago • Mark Cowley

coreMps, author = "setsu sahara", + email = "sahara at salk.edu", + biocViews = "AnnotationData", + organism = "Mouse", species = "mouse", + url = "http://www.salk.edu") > makePdInfoPackage(seed, destDir = ".") = = = = = = = = = = = = = = = = = ====================================================================== == Building annotation package for

BiocViews Annotation Organism biocViews oligo BiocViews BiocViews Annotation Organism

updated 14.7 years ago • Setsuko Sahara

i.e. I get 2442 GO from 642 genes, I want 642 max (some won't have any MF level 2 I think)). > My organism is Plasmodium. I also tried through the org.Pf.plasmo.db package too, but I don't think there is a way to select a specific

GO Organism biomaRt GOSim GO Organism biomaRt GOSim

updated 14.5 years ago • Marc Carlson

an error when using the Bioconductor packages AnnotationDbi and AnnotationForge. I am generating an organism package using the makeOrgPackage function in the AnnotationForge package. To do so, I am using two dataframes: gids

software error AnnotationForge AnnotationDbi

updated 5.8 years ago • jdiaz

with an "org." prefix and are available as SQLite-based packages only. They are the following (5 organisms are currently supported): org.Hs.eg.db: Genome wide annotation for Human org.Mm.eg.db: Genome wide annotation

SNP Microarray SAGE Annotation Bayesian Regression GUI CGH hgu95av2 graph Rgraphviz SNP

updated 18.4 years ago • Hervé Pagès

Hello, I was using BSgenome.Mfascicularis.NCBI.6.0 genome for the [Signac](https://stuartlab.org/signac/articles/pbmc_multiomic) multiomics tutorial. It was working fine until the I was trying to change the name of the chromosomes to match the GTF I have (macFas6-hg38-gencode.v47.basic.sortedgtf). This code worked before ``` mf_genome <- BSgenome.Mfascicularis.NCBI.6.0 # see 1st chrom…

BSgenome.Mfascicularis.NCBI.6.0

updated 12 months ago • Genevieve

samples of the data set, so I guess that is not by coincidence but I don´t see any difference in the organization of data from male and female samples. When I look into the data table within the GSMlist, the beta values are there

GSE61380 GEOquery

updated 3.3 years ago • Carolin

BSgenome BSgenome Rsamtools MEDIPS BSgenome BSgenome Rsamtools MEDIPS

updated 11.9 years ago • Vining, Kelly

was retrieved from dbSNP, from this location to be precise: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat/ (note that the content of this folder has been updated since SNPlocs.Hsapiens.dbSNP.20071016

SNP Cancer SNPlocs SNP Cancer SNPlocs

updated 17.1 years ago • Hervé Pagès

I'm experimenting with custom VCF formats.  More specifically, some colleagues and I are working on establishing standards for polyploid data in non-model organisms. I'd like to make use of the Sample field format as described in the current VCF specification part 1.4.8.  It especially...some colleagues and I are working on establishing standards for polyploid data in non-model…

variantannotation coldata

updated 7.4 years ago • lvclark

The released packages include tools which facilitate: * annotation * data management and organization through the use of the S4 class structure * identification of differentially expressed genes and clustering

Proteomics Annotation Normalization GO Cancer CGH pamr gcrma gpls affyPLM webbioc bim

updated 21.8 years ago • A.J. Rossini

abit stupid). When i try to use Resourcerer with: > >resourcerer2BioC("Agilent_HumanGenome.zip",organism="human",destDir=f ile.path(. path.package("Resourcerer"),"temp"), >pkgName=("AgilentHumanGenome"), srcUrls=getSrcUrl("all

Cancer Resourcerer Cancer Resourcerer

updated 20.6 years ago • John Zhang

0.046129910985666434 0.6341423786636047 GOTERM_BP_FAT GO:0010033~response to organic substance 10 18.51851851851852 6.143711138201849E-4 1410,1281,2625,760,5156,5021,3553,4886,629,4015 47 721 13528...0.04740047867029662 0.724160644743066 GOTERM_BP_FAT GO:0030198~extracellular matrix organization 3 5.555555555555555 0.04867266146190952 1281,5156,4015 47 104 …

Transcription PROcess GOstats cycle Transcription PROcess GOstats cycle

updated 15.6 years ago • zhidong yuan

Hi, I am trying to load the CollecTRI network using decoupleR and am getting the follwing error: Does anybody have any suggestions? Thanks! ```r net = get_collectri(organism='human', split_complexes=False) 2024-06-11 15:13:22] [WARN] [OmnipathR] HTTP 403 [2024-06-11 15:13:22] [WARN] [OmnipathR] Failed to...the follwing error: Does anybody have any suggestions? Thanks! `…

decoupleR OmnipathR

updated 20 months ago • silvaesilva.da

in the mzTab-M format, but I'm not sure how to go about this, particularly with the current level of organization and analysis of the mzML files I am processing. I am iterating hierarchically (site > clone) over the files such

xcms mzTab-M iterativehierarchicalprocessing FBMN

updated 2.7 years ago • Abrianna

<div class="preformatted">I just fixed the problem in AnnBuilder (1.1.3.12). If you can not access the new version here is the solution for now. mySrcUrls <- AnnBuilder:::getSrcUrl("all", "Homo sapiens") then the code should run. The short versions of source files do not work any more due to a switch from LocusLink to Entrez Gene. >X-Original-To: jzhang at jimmy.harvard.ed…

GO Cancer Organism AnnBuilder GO Cancer Organism AnnBuilder

updated 19.1 years ago • John Zhang

rather than previous points in the RNAseq analysis. Quick summary: We are working on a non-model organism, with no genome or transcriptome databases. We are analyzing 4 tissues under 2 treatments, each one in triplicate

deseq2

updated 7.4 years ago • Emiliano Canton

Description: Zea mays full genome as provided by EnsemblPlants (AGPv4, release 32) Version: 4.32 organism: Zea mays common_name: maize provider: EnsemblPlants provider_version: 4.32 release_date: Aug. 2016 release_name

BSgenome

updated 9.4 years ago • ROka

TxDb: <pre> txdb <- makeTxDbFromGFF(file='~/devtestdata/Arabidopsis_thaliana.TAIR10.36.gtf', organism='Arabidopsis thaliana', chrominfo=Seqinfo(seqnames=c('1','2','3','4','5','Mt','Pt'), seqlengths=c(30427671,19698289,23459830,18585056

derfinder genomicfeatures genomicranges

updated 8.5 years ago • fruce_ki

gt;makeLinkedTxome(indexDir = indexDir, source = "Ensembl", organism = "Mus musculus", release = "99", genome = "GRCm38", fasta = fastaFTP, gtf = gtfPath, write = FALSE) >coldata <- read_csv("rnaseq_samples.csv

tximeta

updated 4.9 years ago • dshres

format="gff", + dataSource="TAIR", + organism="Arabidopsis thaliana") Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame

summarizeoverlaps summarizedexperiment count matrix low counts rna-seq

updated 10.1 years ago • shania90.lk

are annotated with information (at least 20 factors, > > could be extended to 50) like the organ from which the RNA was > > extracted, the experimenter that did the lab work, the labelling kit she > > used and a huge

GO limma PROcess GO limma PROcess

updated 16.2 years ago • Yannick Wurm

Hello, I am trying to run swish on a non-reference transcript assembly. I've tried: - Importing the data via tximeta, although I am having trouble getting tximeta to recognise my custom transcriptome (which consists of referenced transcripts from Ensembl.GRCh38.v85 as well as novel transcripts assembled from StringTie). When using a LinkedTxome as follows: ```r #make the linkedTx…

tximeta swish fishpond

updated 4.8 years ago • Jack Riley

<div class="preformatted">Hi Brian, I'm putting this on the mailing list since this might actually affect other users. Brian Herb wrote: > Herve- > > You perviously helped me with building the BSgenome package for the Rat, > and now i am helping my lab mate create a BSgenome package for the > rhesus monkey. We are running into an error when he reads in t…

Cancer BSgenome BSgenome IRanges Cancer BSgenome BSgenome IRanges

updated 16.0 years ago • Hervé Pagès

gmail.com", + biocViews = "AnnotationData", + genomebuild = "GRCh37", + organism = "Human", + species = "Homo sapiens", + url = "") > > makePdInfoPackage(seed, destDir=base_dir); ====================================================================== ========== Building annotation package for

BiocViews Annotation Organism biocViews oligo oligoClasses BiocViews BiocViews Annotation

updated 10.8 years ago • Guilherme Rocha

use the latest bioconductor >>> annotation packages to work around this. You could use an organism >>> based package to map from gene symbols over to entrez gene IDs for >>> instance. Then you could just feed

Annotation biomaRt Annotation biomaRt

updated 18.3 years ago • Marc Carlson

<div class="preformatted">Dear Uli, Thanks for the suggestion. In GWASTools 1.5.9 (which will become the next release very soon), the "snp.annot" argument in convertNcdfGds should be a SnpAnnotationDataFrame, and the chromosome codes from snp.annot will be preserved in the resulting GDS file. best wishes, Stephanie On 1/16/13 2:42 AM, Ulrich Knief wrote: > Dear Stephanie, &gt…

Organism GWASTools Organism GWASTools SNPRelate

updated 12.9 years ago • Stephanie M. Gogarten

srcUrls = mySrcUrls > baseMapType = myBaseType > pkgName = "hsRCv2" > pkgPath = datadir > organism = "Homo sapiens" > version = "1.0.0" > author = list(author = "Barry Henderson", maintainer = "barry.henderson at ribonomics.com...mySrcUrls["UG"], parser = file.path(pkgpath, + "scripts", "gbUGParser"), baseFile = baseName, + organism = "Homo sapiens", buil…

Annotation GO Cancer Organism Biobase annotate AnnBuilder PROcess Annotation GO Cancer

updated 20.5 years ago • Barry Henderson

Link to apply: https://careers-fhcrc.icims.com/jobs/21650/data-scientist-ii/job **Overview** Cures Start Here. At Fred Hutchinson Cancer Research Center, home to three Nobel laureates, interdisciplinary teams of world-renowned scientists seek new and innovative ways to prevent, diagnose and treat cancer, HIV/AIDS and other life-threatening diseases. Fred Hutch’s pioneering work in bone marrow…

bioinformatics opening cancerresearch biostatistics research

updated 4.0 years ago • Fred Hutch (Recruiting)