User: Johannes Rainer

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Johannes Rainer1.3k
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@jotsetung
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PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

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Comment: C: Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
... Just one more note on the EnsDb databases/packages. The package Aaron was using above is based on Ensembl release 86. You should make sure to use annotations from the same Ensembl release throughout your analysis. While the release 86 EnsDb is the most recent one provided as annotation package, you ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I guess so. I've never done that but it should work. ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I just checked the tx IDs in the ncrna and the cdna files and they are not overlapping. So both files contain a different set of genes/transcripts. ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I would assume that most (if not all) ncRNAs are in the ncrna fasta file (e.g. homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz). I've checked and all of the IDs in this file are present in the EnsDb (for Ensembl version 92). ...
written 3 months ago by Johannes Rainer1.3k
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Answer: A: Create Ensembl transcript to gene IDs table with R ensembldb package for tximpor
... Re question 1: To get an overview of all available EnsDb databases for mouse you use AnnotationHub, not ensembldb: > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2018-04-30 > query(ah, "EnsDb.Mmusculus") AnnotationHub with 6 records # snapshotDate(): 2018-04-30 # $da ...
written 4 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Both the EnsDb from the link above and the cdna fasta file are based on Ensembl release 92, so all transcripts from the cdna fasta file should be in the EnsDb. Note however that transcript IDs in EnsDb databases are without the transcript version (e.g. the ".1" in "ENST00001.1"). Did you use ignoreT ...
written 4 months ago by Johannes Rainer1.3k
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Answer: A: Metabolite identification package
... I guess you have already identified the chromatographic peaks/features with xcms, what you could do then is to use the CAMERA package to find adducts and isotopes in your data. Ultimately you will however have to look up the m/z of your peaks in a database (like hmdb (https://hmdb.ca)) to find possi ...
written 4 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Just in case you want the quick and easy way out: you can download the human EnsDb package for Ensembl v92 from: https://www.dropbox.com/s/plne78gvnznwbl7/EnsDb.Hsapiens.v92_2.0.0.tar.gz?dl=0 ...
written 5 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... I'm installing the Ensembl core databases locally and it takes ~ 4-5 hours (depdends on the species, human takes quite a while). If you're querying the databases at Ensembl it might take even longer. ...
written 5 months ago by Johannes Rainer1.3k
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Answer: A: ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTable
... Hi Ramiro, +1 for trying to build an EnsDb on your own. This requires however (as detailed in the vignette) a local installation of the Ensembl Perl API (http://www.ensembl.org/info/docs/api/api_installation.html) along with perl version 5.18.0. The function uses the Ensembl Perl API to query the E ...
written 5 months ago by Johannes Rainer1.3k

Latest awards to Johannes Rainer

Popular Question 3 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
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Appreciated 15 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 15 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 reactome.db: reactome IDs not mapped to pathway names
Guru 15 months ago, received more than 100 upvotes.
Voter 15 months ago, voted more than 100 times.
Scholar 15 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Appreciated 15 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 15 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 15 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Teacher 15 months 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
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 15 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 15 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 15 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 16 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 17 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Scholar 17 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
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Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.4 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Scholar 2.4 years ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 2.4 years ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.4 years ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74

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