use the bioconductor package goseq for go-
term/pathway
enrichment of my expression data.
Since my organism of interest isn't included in the goseq database, I
am
manually entering the data for gene lengths and categories
Order by: Relevance
URGI; v1a) see https://urgi.versailles.inra.fr/Species/Pisum/Pea-Genome-project
Version: 1a
organism: Pisum sativum
common_name: Pea
genome: Pisum_sativum_v1a
provider: URGI
provider_version: Pisum_sativum_v1a
updated 5.2 years ago • sophie.harrington
kgml.path="C:\\Users\\David\\Documents\\R\\win-library\\3
.0\\SPIA\\extdata\\keggxml\\hsa",organism="aag",out.path="C:\\Users\\D
avid\\Documents\\R\\win-library\\SPIA\\extdata\\")
This resulted in [1] TRUE and an aagSPIA.RData file
sequences for Zea mays (AGPv3)
Description: Full genome sequences for Zea mays
Version: 1.0.0
organism: Zea mays
common_name: maize
provider: NCBI
provider_version:
release_date: Oct. 2015
release_name: MaizeGDB
source_url
updated 10.4 years ago • Marcin Grzybowski
<div class="preformatted">Dear all,
Now I am using pathview to map my RNAseq expression data to the
keggmap of my organism 'mez'. I want to know how pathview deal with
the colour of enzyme with several conding genes, for example:
In pathway: Glycolysis...Dear all,
Now I am using pathview to map my RNAseq expression data to the
keggmap of my organism 'mez'. I want to know how pathview dea…
GOSemSim package, but I am getting the following error:
__> mgeneSim(protein\_id\_list, organism="human")__
<0 x 0 matrix>
There were 50 or more warnings (use warnings() to see the first 50)
__> warnings
## __New: Master of Science (Laurea Magistrale) in Quantitative and Computational Biology__
### ___University of Trento, Italy___
a __multidisciplinary degree that formally integrates quantitative sciences and applied biology__, thanks to the following organizations at the University of Trento:
* <a href="http://www.cibio.unitn.it/" target="_blank">CIBIO, Centre for integrativ…
updated 9.6 years ago • enridomenici
<div class="preformatted">Dear Bioconductor Developers and Users,
I have created few annotation packages which are for organism
specific
proteomics database from IPI(http://www.ebi.ac.uk/IPI/IPIhelp.html) .
Now I am keen on writing a generic utility...Dear Bioconductor Developers and Users,
I have created few annotation packages which are for organism
specific
proteomics database from…
updated 18.3 years ago • Chanchal Kumar
<div class="preformatted">Hi all,
actually, I have (a) similar question(s) regarding a very non-
standard
Agilent data set: this is a custom 60mer oligo chip, the probes of
which are
designed from Arabidopsis thaliana sequence information, but intended
to
measure expression in the related non-model organism Arabis alpina.
There are
several probes per A. thaliana gene (not always the same…
updated 18.0 years ago • Ulrike Goebel
are
revolutionizing genetics by allowing us to sequence the genomes of
many
different individual organisms in a population and to observe their
complex coding and non-coding transcriptomes and regulatory events
under
updated 16.0 years ago • Wolfgang Huber
gt; ABPkgBuilder(baseName=myBase,srcUrls=mySrcUrls,baseMapType="ll",
+ pkgName="rats",pkgPath=myDir,organism="Rattus
norvegicus",version="1.1.0",
+
author=list(authors="Alice",maintainer="alice.johnstone at
esr.cri.nz"),fro
mWeb...baseName = myBase, srcUrls = mySrcUrls, baseMapType =
"ll",
pkgName = "rats", pkgPath = myDir, organism = "Rattus
norvegicus",
version = "1.1.0", author =…
updated 18.3 years ago • Johnstone, Alice
Hi everyone,
I have problem in reproducing vignette example from MeSHDbi package.
That is, when I run:
<pre>
> example("makeGeneMeSHPackage")</pre>
It should use preformatted data frames "PAO1" and "metaPAO1" to construct custom org.MeSH.XXX.db package that can subsequently be loaded via library() and queried with Annotation.dbi or RSQLite, or at least that is ho…
updated 10.9 years ago • Ceca Bojic
249")
# Pathway enrichment analysis
enriched_pathways <- enrichPathway(gene = random_genes, organism = "mouse")
# Extract pathway and gene information
pathways <- as.data.frame(enriched_pathways)
`# Create an edge list
updated 20 months ago • Antonio
0.01,
qvalueCutoff = 0.05)
```
returning:
```
#
# over-representation test
#
#...@organism Homo sapiens
#...@ontology BP
#...@keytype SYMBOL
#...@gene chr [1:294] "SORBS1" "PIK3C3" "TBC1D4" "SKP2" "PELI1" "SCIN" "LPL" "SPOPL" "BRAF" "SIRT1
updated 4.3 years ago • samsiljee
indexDir = "/Users/atari/biodata/genomes/ensembl_hg38/indexes/SALMON",
source = "ensembl",
organism = "Homo Sapiens",
release = 98,
genome = "GRCh38",
fasta = "/Users/atari/biodata/genomes/ensembl_hg38/transcripts/ensembl_hg38_transcripts.fa.gz
updated 4.2 years ago • atariw
have done RNAseq and the usual differential gene expression analysis pipelines (Deseq, etc) in one organism under two different conditions and now, we would like to do it between these different bacteria.
We have 2 different
updated 2.0 years ago • Abril
Y and M.
What is chr4_gl000193_random for instance.
Thank you
#=========
Hsapiens
Human genome
|
| organism: Homo sapiens (Human)
| provider: UCSC
| provider version: hg19
| release date: Feb. 2009
| release name: Genome Reference Consortium
updated 11.6 years ago • Asma rabe
Loading required package: RCurl
Loading required package: bitops
extracting only data for our organism from : gene2pubmed
Getting data for gene2accession.gz
Error in sqliteSendQuery(con, statement, bind.data) : 
updated 11.1 years ago • oliver.tills
txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: BioMart
# Organism: Saccharomyces cerevisiae
# Taxonomy ID: 4932
# Resource URL: www.biomart.org:80
# BioMart database: ensembl
# BioMart
updated 10.3 years ago • vinod.acear
from
well-controlled experiments are 0.4 for human data, 0.1 for data on
genetically identical model organisms or 0.01 for technical
replicates. "
But I came across this post which mentions a conservative way to
calculate BCV
clusterProfiler)
> data(gcSample)
> xx <- compareCluster(gcSample, fun="enrichKEGG",
+ organism="hsa", pvalueCutoff=0.05)
> p1 <- emapplot(xx)
Fehler in (function (classes, fdef, mtable) :
unable to find an inherited method
updated 6.1 years ago • rapmic
<div class="preformatted">I regret that I must announce the cancellation of the course announced
below, owing to logistic
difficulties and low turnout for this particular date. When the
course is
rescheduled,
it will be announced on this list.
On Tue, Sep 17, 2013 at 1:10 AM, Vincent Carey
<stvjc@channing.harvard.edu>wrote:
> This two day course is described in a preliminary…
updated 12.4 years ago • Vincent J. Carey, Jr.
Hi all,
I was just wondering if somebody could help me regarding normalized count after DESeq.
I carry out a DESeq on a time course experiment in order to then make a count matrix of significantly expressed genes to look for patterns in gene expression across different samples. However, I have noticed that the count matrix I am making post DESeq on significantly expressed genes are ac…
2.1
| Db type: ChipDb
| Supporting package: AnnotationDbi
| DBSCHEMA: HUMANCHIP_DB
| ORGANISM: Homo sapiens
| SPECIES: Human
| MANUFACTURER: Affymetrix
| CHIPNAME: Human Genome U133 Set
| MANUFACTURERURL: http://www.affymetrix.com
updated 8.0 years ago • Agaz Hussain Wani
2, ..., 10 (total: 10)
geneIdType: Null
collectionType: Null
setIdentifier: MyId
description:
organism:
pubMedIds:
urls:
contributor:
setVersion: 0.0.1
creationDate:
> c(setName(myGset), setIdentifier(myGset)) ;
[1] "MyName...Null
setIdentifier: bdmgWorkstation2:28927:Tue Jan 24 12:09:13 2017:1
description:
organism:
pubMedIds:
urls:
contributor:
…
updated 9.1 years ago • jcrodriguez
of FC values in each condition separately.
<pre>
> viewPathway("Scavenging by Class B Receptors", organism = "human", readable = TRUE, foldChange = cond1FC, vertex.label.font = 3, vertex.label.cex = 0.7, col.bin = 10, legend.x = 1, legend.y...columns</pre>
http://imgur.com/w77zQO4
<pre>
> viewPathway("Scavenging by Class B Receptors", organism = "human", reada…
updated 9.1 years ago • Kajus Baidžajevas
notes)) {
cat("Generating notes from ", fnames[1], "\n", sep="")
row <- grep("Organism", y)[1]
organism <- strsplit(y[row], "=")[[1]][2]
row <- grep("Category", y)[1]
category <- strsplit(y[row], "=")[[1]][2]
row <- grep("Subcategory", y)[1]
subcategory...collapse = ",")
else
parameter…
REVIGO website for some reason, I've been trying to use rrvgo package. I'm working with a non-model organism, so I used Blast2GO to annotate the sequences and obtain their associated GO terms. Also, I created an OrgDbPackage
updated 16 months ago • daccar98
Hsapiens, chrs="chr21", width=250, spacing=250)
> cpgdens <- cpgDensityCalc(windows, organism=Hsapiens, w.function="linear", window=700)
> sI <- matrix(rnbinom(2\*length(windows), mu=5, size=2), ncol=2)
> bm <- BayMethList
updated 10.6 years ago • Matthias Lienhard
and that you provide me the list
of exon level probe sets you are trying to plot and which organism you
are using.
Cheers
Raffaele
--
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze
updated 16.7 years ago • raffaele calogero
<div class="preformatted"> Call for Contributions
=====================================================================
LIFE SCIENCE FREE SOFTWARE SESSION
held at CompLife 2006 (http://www.complife.org)
in Cambridge, United Kingdom, on September 27 - 29, 2006
=====================================================================
In the l…
updated 19.8 years ago • Thorsten Meinl
Hi Bioconductor Support,
Since 2018 I've been interacting with rOpenSci's organizers. For those that don't know, [rOpenSci](https://ropensci.org/) is a non-profit that aims to
> make scientific data retrieval
<div class="preformatted">Hi,
I get the "Error in pathIDsLev1" error when using the gene2pathway
retrain() function.
> retrain(minnmap=30, level1Only="Metabolism", level2Only="Genetic
Information Processing", organism="hsa", gene2Domains=NULL,
KEGG.package=TRUE, remove.duplicates=FALSE, use.bagging=TRUE, nbag=11)
Retrieving KEGG information...gt; retrain(minnmap=30, level1Only="Met…
updated 16.2 years ago • Dick Beyer
but the result is in
line
with the current knowledge of sex-biased gene expression in my model
organism.
I have done some quality control plots, available here:
- Boxplot:
http://www.iee.uu.se/zooekol/pdf/hemiarray_qc_boxplot.pdf
updated 16.8 years ago • Paolo Innocenti
step is for CEOs and
other business leaders to recognize the strategic role that IT plays
within an organization. We all know and love normal radio.
uk - Save Internet Radio.
</div
<div class="preformatted">Hi,
Hope you're fine
I am trying to make whole genome plots using the geneplotter
package/annotate package. The organism I am studying is Arabidopsis
thaliana, and obviously the annotations are not so extensive there:
when
trying to build...re fine
I am trying to make whole genome plots using the geneplotter
package/annotate package. The organism I am studying i…
updated 17.4 years ago • Samuel Wuest
<div class="preformatted">
Hi,
I have a question regarding the minimal number of genes that we can
test in an analysis with edgeR. Let me explain, in a study, edgeR
have been used for testing the differential expression of three
viruses between two conditions, without considering the counts on
other features. That is, the data frame d$counts has only three lines
(and 4 columns, as there i…
is going to be difficult, because there are many
different annotation formats and many different organisms specificity.
It is very frequently necessary to make custom annotations because
users have different questions...you are
seeing above is telling you. To decide whether this is critical or not
depends on your organisms and on the cases where these occur; e.g. in
drosophila, poplar, these are …
updated 12.2 years ago • Nicolas Delhomme
looks great. Would that we had such a resource
(curated,
> current, and growing) for all organisms!
>
> A few questions, if I may:
>
> 1) What role with respect to FlyFactorSurvey do you picture us
taking here
> at...policy?
>
> 4) Is TRANSFAC only for license holders?
>
> 5) Are there any other organism-speci…
updated 13.8 years ago • Vince Schulz
to study the functional (expression) evolution of mammalian genomes across gene types, lineages, organs, cell types, developmental stages, chromosomes and sexes.
The postdoctoral fellow will be funded by a recently awarded...R., Paabo, S., and Kaessmann, H. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348.
 
myBaseType,
+ + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
Error: syntax error
> + organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE,
Error: syntax error
> + author = list(author = "myname", maintainer = "myname at...mySrcUrls, baseMapType =
myBaseType,
+ otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
+ organism = "Homo sapiens", version = "1.…
updated 20.1 years ago • Yong Jiang
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 "control" condition, essentially). Three biological replicates...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 compariso…
updated 3.2 years ago • Dunois
# Group Greeting Cards in R
Are you looking for a fun and personalized way to celebrate a special occasion with a group of friends, family, or colleagues? Group greeting cards in R might be the perfect solution!
With R's powerful data manipulation and visualization capabilities, you can create custom greeting cards that include messages and images from multiple contributors. Here's how it w…
updated 2.6 years ago • carterethan745
Genomics Research (CGR) laboratory in Gaithersburg, MD, is an advanced, fast-paced, high-throughput organization dedicated to the support of molecular, genetic and epidemiologic studies for investigators at the National
updated 3.0 years ago • Wendy
Hello! I have a list of about 6400 differentially expressed genes and I want to perform KEGG pathways enrichment analysis using the clusterProfiler package.
I first did it with the ORA method, using the `enrichKEGG` function and doing it separately on the genes with positive and negative logFC. I got hundreds of enriched pathways with this method, both for the up and downregulated genes.
I then…
updated 5.1 years ago • Emilia
I have, it seems to be working fine for all except for one dataset. This dataset is from the organism fly while the others are either mouse or human.When I run deseq2 with 'LRT' for the fly dataset I get the following
Hi
I have RNA seq data for six different treatments (A,B,C,D,E,F) of a model organism, with four-fold biological (NOT technical) replicates.
FASTQC revealed no abnormalites in the RNAseq data and after
updated 9.2 years ago • wd
analysis using enrichGO function through clusterProfiler.
As I am going to analyze nonmodel organism seabream so I used AnnotationHub to build OrgDb.
I retrieved the annotation database
library(AnnotationHub)
hub
updated 5.8 years ago • bnajafpour
baseName = "GEM.txt", srcUrls = mySrcUrls, baseMapType
=myBaseType, pkgName = "GEM",pkgPath = myDir, organism = "Mus
musculus", version = "1.0.0",author = list(authors = "joe", maintainer
="joe.joe at gmail.com"), fromWeb = TRUE)
after the creation
updated 18.5 years ago • claudio.is@libero.it
MoGene data collected for mouse using the
following
command:
res = spia(de = DE, all = ALL, organism = "mmu", nB = 2000, plots =
FALSE,
beta = NULL)
The procedure runs to completion and produces results and shows
several
pathways
but as far as we are able to
understand the packages use the info available in the corresponding
organism .db0 packages. However, it is not clear to us how now to
continue with the mirna.db SQLite file we created.
Any advice
updated 16.3 years ago • Guido Hooiveld
with only one ORF sequence per gene.
P.P.S. Alternative splicing isn't a consideration for this organism
Analyst
The EMMES Corporation, organized in 1977, is a privately owned
Contract Research Organization (CRO) located in Rockville, Maryland.
EMMES is dedicated to providing statistical and epidemiological
expertise
updated 17.4 years ago • Marcella Pickard
Hello,
I have been conducting pathway analysis on my RNA-seq data using the Deseq2/GAGE workflow. I ran GAGE and it worked well generating a list of affected pathways. I used “KO” annotations from kegg.gsets (species=”ko”) as I am working on a non-model organism. I am now trying to extract data for essential member genes in my perturbed pathways with essGene() However, I keep getting...pathways.…
updated 9.3 years ago • Michael
F,prefix="primeview",fileName="primevie
wHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANISM
"="Homo
sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="Pri
meView
Human Gene Expression
Array","MANUFACTURERURL
updated 12.9 years ago • wang peter
baseName=myBase, srcUrls=mySrcUrls,
baseMapType=myBaseType,
pkgName="PRG_protein_pkg", pkgPath=myDir,
organism="Oryza sativa", version="1.1.0",
author=list(author="Ross", maintainer="ross.chapman at xxxxxxxx"),
fromWeb=FALSE)}
date()
Can
updated 19.9 years ago • ross.chapman@dpi.vic.gov.au
2) Make sure you have have the appropriate BSgenome.* package which
has the genomic sequence for the organism you are working with. For
instance, if you are working with human data with the hg19 release,
you'd need the BSgenome.Hsapiens.UCSC.hg19
not
meant
to be a way to get a newer package. It is meant to allow people who
are
using non-model organisms to get annotations. So it is expected that
some things are definitely going to be missing unless you want to do
the...either, because that would break a lot of
software
that depends on GO.db being in sync with the organism packages. The
only way around that would be if you also generated…
updated 14.0 years ago • Marc Carlson
Chromosome names of query and genome do not match
> head(BSgenome,100)
1 function (organism, common_name, genome, provider, provider_version,
2 release_date, release_name, source_url, seqnames, circ_seqs...seqinfo)
11 if (missing(common_name))
12 common_name <- species
13 metadata <- list(organism = organism, common_name = common_name,
14 genome = ge…
updated 4.1 years ago • alexandre.maucuer
function calls ... OK
* checking R code for possible problems ... NOTE
.onLoad: warning in BSgenome(organism = "Saccharomyces cerevisiae
SK1",
species = "Yeast", provider = "Hochwagen Lab", provider_version =
"1.00", release_date = "Unsure...extdata_dir): partial argument match of
'seqs_dir' to 'seqs_dirpath'
.onLoad: warning in BSgenome(organism = "Saccharomyces cerevisiae
SK1",
species …
updated 11.8 years ago • Guest User
Recent ...
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