after having successful started my
analysis with the SPIA package.
res1.5=spia(summarized1.5, all, organism="mmu", plots=T)
Done pathway 1 : RNA transport..
Done pathway 2 : RNA degradation..
Done pathway 3 : PPAR signaling pathway..
Done
Order by: Relevance
setReadable<-
Example for groupGO function fails:
data(gcSample)
yy <- groupGO(gcSample[[1]], organism="human", ont="BP", level=2)
Loading required package: org.Hs.eg.db
Error in setReadable(x) <- readable :
could not find function
updated 12.5 years ago • Guest User
that are makefile rules) with the same original versions.
I was wondering if someone else organizes pipelines in a manner similar to ours and has faced the same issues. I am thinking about linking our makefile management
updated 9.6 years ago • Elena Grassi
BTN3A3,MYBL1,GZMA,ARL4C,SH2D1A,TXK,CD7,RORA,CD247,IL18RAP,CD
96
,RASGRP1,GZMM,TRD@,MATK,ITGAL,KLRB1" organism="Human" standard_name="GNF2_ZAP70" systematic_name="c4:526" tags=""></geneset>
==> /data/PathDB/msigdb_v2.5.xml <==
<geneset...PIP5K3,ATM,PIK3C2A,PIK3C3,PIK3CA,
PI
K3CB,PIK3CG,PIK3R2,PIK3R3,IPPK,PI4KA,PI4KB,PI4K2A,ITPKA,ITPKB" organism="Homo sapiens" standard_…
updated 17.6 years ago • Vladimir Morozov
object (has for human, mmu
for mouse):
Mset = new("MEDMEset", pos=pos, chr=chr, logR = logRmat,
organism="hsa")
I am sorry but I did not understand the second point, as "weighting of
MeDIP enrichment" and determination of probe...for N samples
> > rownames(logR) = letters[1:4] # probes are named a,b,c,d here
> > organism = "hsa" # for human or "mmu" for mouse
&am…
updated 17.0 years ago • Prashantha Hebbar Kiradi [MU-MLSC]
nbsp; Establish three new community gardens to provide access to fresh produce within two years.
Organize community fitness events such as walking groups, yoga classes, and sports leagues. Partner with local schools to
updated 15 months ago • Arthurella
Warning message:
In file(con, "r") :
cannot open URL 'https://www.uniprot.org/uniprot/?query=organism:9606&format=tab&columns=id': HTTP status was '400 Bad Request'
Actually this occures specifically when I run
updated 3.4 years ago • Mohamed
BFC")
setTximetaBFC(BFCdir)
makeLinkedTxome(indexDir = index_dir,
source = "gencode",
organism = "human",
release = "v31",
genome = "GRCh38",
fasta = fasta_file,
gtf = gtf_path,
write = FALSE)
txi.methname <- tximeta(s, type = ftype
updated 3.2 years ago • Hasher
Hi,
As other users encountered as well: There is no information available on cytobands for my organism.
Specifically, I'm plotting chr12 of bosTau6 giving me an empty ideogram, which is fine.
<pre>
gen <- "bosTau6"
chr <...nbsp;
As other users encountered as well: There is no information available on cytobands for my organism.
Specifically, I'm …
updated 11.1 years ago • Ludwig Geistlinger
Hello. I'm familiar with DESeq2 but the most complex design equations I've used are having blocked pairs. I need to perform a more complicated design but I'm having trouble formulating the equation. I have a design table that I've read in that contains all the relevant information. Here are the specifications:
condition = sample/control (what I'm testing over)
week = a timepoint comparis…
as Biostrings object ("BSgenome.Celegans.UCSC.ce10"), and a Hi-C dataset available online from this organism, and it worked.. so I think that the problem should be related to the input of my genome as fasta file, but CutGenome function
updated 10.5 years ago • rulicosentino
standard database schema."
Problem I face now is which database scheme to use.
For the well-studied organisms like human, mouse, pig, etc a scheme is
available, but for Chinese Hamster that is not the case.
As test I just used the
updated 12.3 years ago • Guido Hooiveld
Hi,
I'm doing a study that analyzes RNA-seq results from mouse and _Candida albicans_. For each organism, I have six different conditions. For a pathway analysis I used the Pathview package with the multi-state option...Hi,
I'm doing a study that analyzes RNA-seq results from mouse and _Candida albicans_. For each organism, I have six different conditions. For a pathway analysis I used the Path…
updated 10.0 years ago • daniel.molecular
in the right place and form :-)
According to the PANTHER.db information
PANTHER.db object:
| ORGANISMS: ...
| PANTHERVERSION: 12.0
| PANTHERSOURCEURL: ftp.pantherdb.org
| PANTHERSOURCEDATE: 2017-Sep15
| package: AnnotationDbi
updated 6.9 years ago • alfonsosaera
__Job description:__
Panorama Medicine is seeking an experienced RNA Computational Biologist with a strong RNA biology background to analyze large-scale RNA data at their Philadelphia office.
__Responsibilities:__
Analyze large-scale RNA-seq data. Discover underlying mechanisms of observed data results. Closely work with molecular biologist for target validation.
__Minimum Qualifications:__
…
Can someone please help to debug this error using the gseKEGG function in clusterProfiler ?
__This is how I prepare the ranked gene list__
> y=geneset$log2FoldChange
> names(y)=as.character(geneset$Entrez\_Gene\_ID)
> y<-sort(y, decreasing=TRUE)
> head(y)
362893 29219 116568 &n…
updated 8.4 years ago • bruno.saubamea
Hi,
I am trying to address the question which genes associate with change of the metabolite levels following the diet. I have paired samples (before and after the diet). I have previously asked about possible adjustments to the paired set (https://support.bioconductor.org/p/134040/#134068) so just few follow up questions
That is an example of my data organization.
```
Sample ID Timepoint …
updated 5.2 years ago • anna.cot.anna.cot
filesDirectory="/projects/EASYRNASeq/",
+ gapped=F,
+ validity.check=TRUE,
+ chr.map=chr.map,
+ organism="custom",
+ annotationMethod="gff",
+ annotationFile="/projects/ZmB73_5b_FGS.gff3",
+ count="genes",
+ filenames=files,
+ summarization
updated 12.8 years ago • Guest User
setup with DESeq2.
In brief, the experiment is about multiple stressor effects in stream organisms, whereby different stressors (here: added sediment, increased salinity or reduced flow velocity) are applied to...the study organisms, either as single stressors or in each possible combination.
I would like to know, which gene expression patterns
updated 4.1 years ago • Marie
R
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'BSgenome(organism = "Toxoplasma gondii", ': unused arguments (nmask_per_seq = .nmask_per_seq, masks_pkgname = pkgname, masks_dir = extdata_dir...onLoad failed in loadNamespace() for 'BSgenome.Tgondii.ToxoDB.7.0', details:
call: BSgenome(organism = "Toxoplasma gondii", species = "Toxoplasma gondii",
e…
updated 4.8 years ago • ms_toxo
Hi everyone,
I would be very grateful for your advice on the experimental design described below. Perhaps @gordonsmyth could also share his thoughts.
I generated a pseudobulk expression matrix from scRNA-seq data. The design can be described as a 3-factor setting:
- Regions: 2 sampled regions from the same tissue/organ
- Disease condition: 2 groups (15 healthy vs. 15 diseased donors)
- C…
Apologies for cross-posting on biostars, but the part most relevant to me involves procedures using Bioconductor packages.
I'm working on a haplotype-resolved diploid assembly of a plant genome, where each chromosome is represented by two FASTA/GTF pairs rather than a single consensus. I want to carry out Bulk RNA-seq count-based differential expression analysis with Bioconductor (e.g. limma, ed…
multidisciplinary collaborations
addressing fundamental biological questions in model and non-model
organisms. The research
emphasis should be on integrative approaches, such as systems biology,
networks analysis,
comparative
updated 18.2 years ago • Thomas Girke
preformatted">Hi bioc,
I'm having trouble with the problem of creating the annotation package
for
organism = human, array type = custom array, and I it'll really be
nice to
get some help at this point.
Here is what I've done so far without
updated 12.3 years ago • gabriel teku
In the <code><strong>Path2PPI</strong></code> package [vignette](http://bioconductor.org/packages/release/bioc/vignettes/Path2PPI/inst/doc/Path2PPI-tutorial.html), section 2.1., the list of proteins associated with the pathway of interest (_i.e._ "autophagy induction") for yeast and human are provided in two named character vectors _“yeast.ai.proteins” _and "_hum…
updated 7.9 years ago • moldach
suggestions for this error.
```
> BSgenome.Rhinella.marina.UNSW.RM170330
cane toad genome:
# organism: Rhinella marina (cane toad)
# provider: UNSW
# provider version: RM170330
# release date: Mar. 2018
# release name: Rhinella
functions in
the lumi package. As for the functions of modeling methylation status,
I
will organize and upload them to the developing version within next
few
weeks, hopefully by the end of this year. For the Illumina
updated 15.1 years ago • Pan Du
Goodger",
email = "cei at ebi.ac.uk", biocViews = "AnnotationData",
genomebuild = "mm9",
organism = "Mus musculus", species = "Mouse")
makePdInfoPackage(seed, destDir=".")
======================================================================
==========
Building annotation package for Affymetrix Gene
updated 16.6 years ago • Cei Abreu-Goodger
statistical methods to high throughput biology and, as part of this
activity, will contribute to the organization and presentation of
training courses in statistics and data-mining. The position includes
the opportunity
updated 18.9 years ago • Wolfgang Huber
td>
<td>7851558</td>
</tr>
</tbody>
</table>
...... and 64 more rows like this
How should I organize the input file? what is the code to run in R?
Thanks
Maria
 
updated 7.5 years ago • adriana.gallego.02
url)
6: .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
5: KEGGREST::keggLink("pathway", organism)
4: kegga.default(de = DEGenes, universe = universe, ...)
3: kegga(de = DEGenes, universe = universe, ...)
2: kegga.DGEExact(et, species
T)
ug <-
UG(srcUrl=ugUrl,parser=file.path(pkgpath,"scripts","gbUGParser"),baseF
ile="geneNMap",
organism="Homo sapiens",built="N/A",fromWeb=T)
srcObjs[["eg"]] <- eg
llMapping <- parseData(eg,eg at accession)
sessionInfo()
R version
<div class="preformatted">Hi guys,
I'm trying to use the function "count" in easyRNASeq to get a
SummarizedExp to be used with DESeq2.
I'm aware it's in active development, so just flagging this up in case
I'm just doing something wrong
Here's what I've done
bamfiles<-dir("RNAseq/BAM files/", pattern="bam$")
conditions <- c(rep("treated",8),rep("normal",8))
names(conditions)…
updated 12.3 years ago • Lescai, Francesco
<div class="preformatted">re: '[BioC] question about Gviz' thread fallout:
Yesterday I rolled a relatively simple programmatic way to label UCSC
KnownGene entries with their symbols. However, some isoforms (e.g.
some
for NRIP1 and CDKN2B) seem to be missing from the mappings.
Investigating a bit, and referring to ?org.Hs.egUCSCKG, I find
...This mapping is based on the very latest buil…
updated 12.9 years ago • Tim Triche
thought.
- Excellent oral and written communication skills.
- Excellent time
management, task organization, and multi-tasking skills.
- Good
understanding of molecular biology, genetics, and immunology.
- Deep
understanding...immunology breakthroughs into clinical therapies and healthier patients.
As a non-profit organization within the Virginia Mason Health System, BRI over…
updated 4.1 years ago • hbolouri
amp; Nano-fluidics
- Pre-analytical Steps
- qPCR BioStatistics & BioInformatics
The scientific organization is managed by an internationally renowned
scientific advisory board in the field of quantitative real-time...scientific coordinator of the Symposium and the Application
Workshops qPCR2011@wzw.tum.de
Event organization: Dr. Martina Reiter, BioEPS GmbH, Freising,
Germany Mart…
KEYWORDS Pseudomonas Genome DB Version: 19.1.
SOURCE Pseudomonas aeruginosa
ORGANISM Pseudomonas aeruginosa
.
FEATURES Location/Qualifiers
pseudo 1..805
/gene="filamentous hemagglutinin (pseudogene...KEYWORDS Pseudomonas Genome DB Version: 19.1.
SOURCE Pseudomonas aeruginosa
ORG…
lists and p values from a DESEQ2 output and loading that as a genelist, along with a GO file for my organism as follows;
```r
# extract the adjusted p-values from our results object
geneList <- res$padj
# add the gene names from our
Does Pathview not work
with Bacillus subtilis subsp. subtilis 168 (=bsu) even
though it's a KEGG organism? Or what am I doing wrong?
I look forward to hearing from you.
Sincerely yours,
David
</div
updated 11.9 years ago • Luo Weijun
gt;
> Here's how I used the easyRNASeq function:
>
> DGElist = easyRNASeq(organism="Hsapiens",
> annotationMethod="biomaRt",
> gapped=TRUE,
> count="genes",
> summarization="geneModels",
> file…
updated 12.9 years ago • delhomme@embl.de
dataSource="gff3 from 12SD80 000036F primary contig",
organism="Puccinia coronata")
#Subset to just genes
wh <- subset(genes(txdb))
#Make plot of just gene track in the region of interest
updated 7.2 years ago • marisa.e.miller
pre>
txdb <- makeTxDbFromGFF("/pathto/gencode.v19.annotation.gtf", dataSource="Gencode", organism="Homo sapiens", format="gtf")</pre>
<pre>
txdb_5utr_transcript <- fiveUTRsByTranscript(txdb, use.names=T)
txdb_exons_transcripts
updated 8.6 years ago • Walter F. Baumann
pcbi.upenn.edu="">
Maintainer: Elisabetta Manduchi <manduchi at="" pcbi.upenn.edu="">
License: GPL-3
organism: Sus scrofa
species: Pig
provider: UCSC
provider_version: susScr2
release_date: Nov. 2009
release_name: SGSC Sscrofa9.2
updated 14.2 years ago • Elisabetta Manduchi
distinguish cis and trans regulatory divergence between close species, and it is widely used on many organisms. The trick is that we profile gene expression in the two species and their F1 hybrid. We then determine allele-specific
updated 5.7 years ago • gat.krieger
to run dexseq_prepare_annotation.py on a gtf file (Ensembl
version) downloaded from iGenomes. The organism is Arabidopsis
thaliana. I am constantly getting error messages that look like this:
Traceback (most recent call
currently supported by multiple types of funding, such as NIH and other federal grants, non-profit organization grants, funds from industry, and funds from philanthropic donors.</a>
Johns Hopkins University is a leading institution
updated 8.1 years ago • cleo.k.yang
0.99.0",
email = "myemail@jhu.edu",
biocViews = "AnnotationData",
genomebuild = "HG 18", organism = "Human",
species = "Homo sapiens")
makePdInfoPackage(seed, destDir = ".")
*After the code worked for 2 hours, I got these errors
updated 13.7 years ago • zeynep özkeserli
<div class="preformatted">I apologize up front to Valarie for posting additional questions
related
to her excellent read counter. This time my questions are related to
the
economics of accessing big files as few times as possible to improve
workflow performance in large RNA-Seq projects and to subsequently
allow
deleting all input bam files since BIG DATA is killing us :).
(1) What is curr…
Hi,
I have a problem with adding REFSEQ IDs to the SummarizedExperiment object, containing ENSEMBL transcripts and quantification information from Salmon. I have a tximeta_1.0.3 version. I used makeLinkedTxome:
indexPath <-"/usr/users/asawick/ania/U2OS_4sU_060319/salmon/Homo_sapiens.GRCh38.cdna.all_index"
fastaPath <-"/usr/users/asawick/ania/U2OS_4sU_060319/salmon/Homo_sapiens.…
updated 6.7 years ago • anna.sawicka
Any one has encountered this error. What might be the problem.
<pre>
kk=enrichKEGG(gene=genes, organism="human", pvalueCutoff=0.05, pAdjustMethod="BH", qvalueCutoff=0.1, readable=FALSE)
Error in .getUrl(url, .listParser, nameColumn
updated 9.9 years ago • 1992
Hi all,
i am trying to build a BSgenome package for olea europea for some Medipseq analysis , i run the first command
<span style="background-color:Yellow"><code>library(BSgenome)<br/>
> forgeBSgenomeDataPkg("path/to/my/seed")</code></span>
it working and creating<code> <strong>the single_sequences.2bit</strong></code>
the when i r…
updated 7.2 years ago • oussama.badad
Hello everybody,
I was trying to create a TxDb from a custom gtf for some analyses.
I found out that ___makeTranscriptDbFromGFF___ was replaced for the newer ___makeTxDbFromGFF___, so I decided to try this function. To my surprise I got no error with the following code (see below), but when I inspected the TxDb (I saved it to a .sqlite file) It was almost empty (had only the "chrominfo" and "…
updated 10.2 years ago • José Luis Lavín
<div class="preformatted">There is already a bovine.db0 package in the development branch of
bioconductor. I didn't call it cow.db0 because I didn't want any
"bull.db0" in the repository. (Please forgive the pun about
"bull.db0",
I just could not resist.) ;) A chicken.db0 database is already
planned to be added as well.
As for the question about code for making your own source databas…
updated 17.3 years ago • Marc Carlson
lt;- dotplot(tissueCompare, showCategory = c("response to bacterium", "defense response to other organism", "response to cytokine", "innate immune response", "cellular response to cytokine stimulus")) #top 5 GO BPs of interest
return
updated 4.1 years ago • Jordan
of major GOs.
I also tried with the "groupGO" but the problem is that in the "OrgDb" object the organism that I have worked with is none of the options so I dropped it from the code.
Just to clarify a few more things, the common
updated 3.6 years ago • Noy
<div class="preformatted">I am trying to run the following codes from AnnBuilder Vignette in R
2.2.1
under Windows XP,
######################################################################
###
library(AnnBuilder)
read.table(file.path(.path.package("AnnBuilder"),"data","thgu95a"),sep
="\t",
header=FALSE,as.is=TRUE)
myBase<-file.path(.path.package("AnnBuilder"), "data", "thgu95a")
…
updated 19.8 years ago • Xue Lin
its pity that your recent version does not work properly due to you have updated some functions and their arguments.
\#\# changes in some functions that you made:
In bitr function:
previous it was "annoDb="org.Dr.eg.db"" and now it become "OrgDb".
In enrichGO function:
previous it was organism="zebrafish" " and now you changed into "OrgDb".
Note: Anyway i ma…
updated 9.1 years ago • unique379
there is not a 1-1 correspondence. Ensembl and
NCBI
(the curator of RefSeq) are independent organizations, each with
different
build policies and annotation processes for transcripts. So, in
general in
this field
updated 16.4 years ago • mauede@alice.it
class ("?GenotypeData"),
there
is an example of how to set up GWASTools with a non-human organism.
I am copying the Bioconductor mailing list. Please include
bioconductor at r-project.org if you have any follow
listDatabases() # as expected
keggList("pathway") # no go
keggList("hsa") # no go
keggList("organism") # gives an answer</pre>
The error is always:
<pre>
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) :
invalid request
updated 9.8 years ago • Bryan Hanson
Recent ...
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