User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.2k
Reputation:
1,180
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Location:
Italy
Twitter:
@jotsetung
Last seen:
9 hours ago
Joined:
3 years, 3 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 225 results • page 2 of 23 • next >
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News: Ensembl 91 EnsDb databases added to AnnotationHub
... Dear all, EnsDb databases (for ensembldb) for Ensembl release 91 are available for current Bioc3.7 (devel). > library(AnnotationHub) > query(AnnotationHub(), "Ensembl 91 EnsDb") snapshotDate(): 2017-12-21 AnnotationHub with 88 records # snapshotDate(): 2017-12-21 # $dataprovider: Ensembl # ...
annotation news ensembl ensembldb written 8 weeks ago by Johannes Rainer1.2k
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Comment: C: Error : object path is not exported by namespace:Rsamtools
... Thanks for reporting! I'll look into it. ...
written 9 weeks ago by Johannes Rainer1.2k
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News: Map between protein and genome coordinates using ensembldb
... ensembldb version 2.3.2 (Bioconductor developmental version) provides functions to map between genomic, transcript and protein coordinates. Check the coordinate-mapping vignette! ...
annotation news ensembdb written 11 weeks ago by Johannes Rainer1.2k
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Comment: C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
... Might be a problem in the makeTxDbFromGFF function from the GenomicFeatures package. It works with the ensDbFromGtf from the ensembldb package. > library(ensembldb) > dbf <- ensDbFromGtf("Oryza_sativa.IRGSP-1.0.37.gtf.gz") Importing GTF file ... OK Processing metadata ... OK Processing ge ...
written 12 weeks ago by Johannes Rainer1.2k
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Comment: C: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
... Just to avoid confusion: AnnotationHub is a central repository for annotation resources. AnnotationHub contains many different databases among those EnsDb databases, TxDb databases, genomic sequences etc. I wouldn't call them AH#### databases, the AH#### is just the ID of the resource in AnnotationH ...
written 12 weeks ago by Johannes Rainer1.2k
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Answer: A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
... Regarding annotations of mitochondrial genes - if you're interested in Ensembl IDs (or have Ensembl gene IDs) you might give ensembldb and EnsDb databases a try. You can fetch mitochondrial genes from an EnsDb: > library(EnsDb.Hsapiens.v75) > gns <- genes(EnsDb.Hsapiens.v75, filter = ~ se ...
written 3 months ago by Johannes Rainer1.2k
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Answer: A: ReadMSData problem with xcms
... readMSData with mode = "inMem" (the default) will by default read only MS level >= 2 from the input files. If you are going to use xcms you should use readMSData(temp, pdata = pheno, mode = "onDisk") which will a) read all MS levels from the input file and b) return a OnDiskMSnExp object that you ...
written 3 months ago by Johannes Rainer1.2k
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Comment: C: Package won't recognise raw data files
... Did you move the original CDF files after having performed the peak detection? what is the output of filepaths(xsaF) (assuming xsaF is an xcmsSet object)? And can you please provide the output from sessionInfo()? ...
written 3 months ago by Johannes Rainer1.2k
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Answer: A: get_gene_transcript_exon_tables.pl extremely slow
... Hi Ed, using the perl scripts and the Ensembl perl API is indeed very slow. It is even worse if you fetch the data from the main Ensembl MySQL servers. What I am doing with each new Ensembl release is to download first the MySQL database dumps from Ensembl and install them locally. This improves pe ...
written 3 months ago by Johannes Rainer1.2k
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Comment: C: 'names' attribute [12] must be the same length as the vector [6]
... Without getting hands on the data it is pretty hard to say what's going on and where the problem is. ...
written 3 months ago by Johannes Rainer1.2k

Latest awards to Johannes Rainer

Scholar 8 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 8 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 9 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 10 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Scholar 10 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 22 months ago, created an answer that has been accepted. For A: Missing SYMBOL keytype in EnsDb.Hsapiens.v75
Scholar 22 months ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 22 months ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 22 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: biomaRt no longer works with proxy after upgrade
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Centurion 2.2 years ago, created 100 posts.
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.3 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.3 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
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Scholar 2.3 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.

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