User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.5k
Reputation:
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Location:
Italy
Twitter:
@jotsetung
Last seen:
2 days, 7 hours ago
Joined:
5 years, 1 month ago
Email:
j**************@eurac.edu

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

 

Posts by Johannes Rainer

<prev • 278 results • page 2 of 28 • next >
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News: ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
... Dear all, We've just added ensembldb `EnsDb` databases containing annotation from Ensembl for all 169 species in Ensembl release 97 to `AnnotationHub`: ``` > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2019-05-02 > query(ah, c("EnsDb", "v97")) AnnotationHub with 169 ...
annotation news ensembl ensembldb written 4 months ago by Johannes Rainer1.5k
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Comment: C: Best alternative annotation package to BiomaRt
... You are right, the `EnsDb` databases that I provide as a *package* are outdated. But you can get `EnsDb` databases from `AnnotationHub` for all Ensembl releases from version 87 on: ``` > library(AnnotationHub) > library(ensembldb) > ah <- AnnotationHub() snapshotDate(): 2019-05-02 > ...
written 5 months ago by Johannes Rainer1.5k
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Answer: A: Gene biotype for a given symbol
... You can get that information using `ensembldb`: Assuming you're working with human annotations and want to use Ensembl release 86: ``` library(EnsDb.Hsapiens.v86) edb <- EnsDb.Hsapiens.v86 ## Get the transcript biotype for the gene SMC4 genes(edb, filter = ~ symbol == "SMC4", return.type = "Da ...
written 5 months ago by Johannes Rainer1.5k
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Comment: C: Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens
... Just a small comment to James' excellent answer: if your alignment/gene annotations were based on a specific Ensembl release, you should also ensure that you are loading/adding annotations from the same release. Example, your object is based on Ensembl release 91 data, then you would want to get the ...
written 8 months ago by Johannes Rainer1.5k
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Comment: C: mzR unable to open uncorrupted mzXML file
... Before digging into the error message I would make sure that you have all the most recent package versions and that all files are really there. So, please run `BiocManager::install()` to update potentially outdated packages and then `all(file.exists(files))`. You say you have ~ 1500 files, so mayb ...
written 8 months ago by Johannes Rainer1.5k
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Job: Postdoctoral researcher in Computational Metabolomics
... Dear all, Eurac Research is looking for a ## Postdoctoral researcher in Computational Metabolomics The Institute for Biomedicine is seeking a highly motivated researcher to join the Computational Metabolomics team. The Institute for Biomedicine is home to an international and interdisciplinary te ...
metabolomics xcms job written 9 months ago by Johannes Rainer1.5k
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Comment: C: How to use EnsDb in annotatePeak from package "ChIPseeker"
... `intronsByTranscript` is exported in ensembldb version 2.6.6 which will be available in a few days. ...
written 9 months ago by Johannes Rainer1.5k
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Answer: A: How to use EnsDb in annotatePeak from package "ChIPseeker"
... The reason is that `ensembldb` doesn't have an `intronsByTranscript` method. I'll add that and it *should* work. cheers, jo ...
written 9 months ago by Johannes Rainer1.5k
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Answer: A: Retrieve canonical transcript for each gene via ensembldb R package
... At present I am not including this information to the ensembldb databases. So there is no way to get the canonical transcript for a gene using ensembldb. Sorry for that. ...
written 10 months ago by Johannes Rainer1.5k
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Comment: C: Troubles with mzR and BiocInstaller
... Also, the message is rather a warning than an error. mzR will most likely work as expected.   ...
written 11 months ago by Johannes Rainer1.5k

Latest awards to Johannes Rainer

Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 10 months ago, created an answer that has been accepted. For A: Ensembl plants at annotationHub?
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieve canonical transcript for each gene via ensembldb R package
Popular Question 13 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 13 months ago, created a question with more than 1,000 views. For How to get from xcmsRaw to a xcmsSet
Popular Question 13 months ago, created a question with more than 1,000 views. For Reading alignments above a mapq threshold from BAM files
Scholar 13 months ago, created an answer that has been accepted. For A: biomaRt package problem
Popular Question 14 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 15 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Popular Question 18 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 18 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 2.5 years ago, received more than 100 upvotes.
Voter 2.5 years ago, voted more than 100 times.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 2.5 years ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 2.5 years ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 2.5 years ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Scholar 2.5 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 2.5 years ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function

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