User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.3k
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@jotsetung
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1 day, 12 hours ago
Joined:
3 years, 7 months ago
Email:
j**************@eurac.edu

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

 

Posts by Johannes Rainer

<prev • 237 results • page 2 of 24 • next >
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Comment: C: Using massifquant for peak detection of generic matrix data?
... I haven't tried that yet, sorry. ...
written 3 months ago by Johannes Rainer1.3k
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Answer: A: Using massifquant for peak detection of generic matrix data?
... The peak detection algorithms in xcms perform peak detection in retention time domain, i.e. in one dimension of the 2D matrix - with a lot of assumptions on peak shape, scattering of values in one dimension etc. I would have a look at the yamss package instead. AFAIK, yamss uses a two-dimensional k ...
written 3 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb from M.musculus NCBI37 v67 gtf
... Thanks for reporting! ...
written 4 months ago by Johannes Rainer1.3k
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Comment: C: Correct version of EnsDb.Hsapiens for ensembl transcriptome
... I agree with Mike, you're using the same Ensembl release, so you can expect that, even if the version number on the tx ID is not present in the EnsDb, they refer to the same transcripts. Ensembl is quite strict and consistent with their IDs.   ...
written 4 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb from M.musculus NCBI37 v67 gtf
... Very nice. Regarding the problem to fetch the seqlengths - it worked for me - I guess your problem might be related to some network problems?   The warning also suggests this: 2: In download.file(url = paste0(base_url, "/", file_name), destfile = tmp_file,  :   InternetOpenUrl failed: 'The login r ...
written 4 months ago by Johannes Rainer1.3k
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Comment: C: ensembldb from M.musculus NCBI37 v67 gtf
... Thanks for the sessionInfo. In a couple of days you'll be able to install ensembldb version 2.2.1 which would allow you to import the GTF file. Let me know if you run into other troubles. ...
written 4 months ago by Johannes Rainer1.3k
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Answer: A: ensembldb from M.musculus NCBI37 v67 gtf
... I could replicate your error. Apparently, the GTF file from Ensembl version 67 does not contain a field with the exon ID. Thus the function failed once it tried to extract these IDs. I fixed by generating artificial exon IDs in such cases (by concatenating the transcript ID and the index of the exon ...
written 4 months ago by Johannes Rainer1.3k
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Answer: A: ensembldb from M.musculus NCBI37 v67 gtf
... Instead of ensembldb you could use the GenomicFeatures package to create a TxDb object from the GFF (using makeTxDbFromGFF) - this should provide you the same information than an EnsDb. To replicate (and fix) the problem you encounter in ensembldb it would be nice if you could provide the output of ...
written 4 months ago by Johannes Rainer1.3k
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Comment: C: how to get intron with ensembldb. package?
... I'd say your approach seems to be pretty OK. There is no intron ID stored in the database, so you can't get that from an EnsDb. ...
written 5 months ago by Johannes Rainer1.3k
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Answer: A: ensembldb and pseudogenes mapping to the same Ensembl ID
... Dear Meeta, mapping between Entrez and Ensembl IDs is always problematic. EnsDb databases provide you with all the information from Ensembl (for a specific release) and in version 79 (March 2015) this one gene was annotated to two Entrez identifiers. Unfortunately, in EnsDb databases, there is no a ...
written 5 months ago by Johannes Rainer1.3k

Latest awards to Johannes Rainer

Teacher 12 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
Appreciated 12 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 12 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 12 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 12 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 12 months ago, received more than 100 upvotes.
Voter 12 months ago, voted more than 100 times.
Scholar 12 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 12 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 12 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 12 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Teacher 12 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
Scholar 12 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 12 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 13 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 14 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Scholar 14 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
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 2.2 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Scholar 2.2 years ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 2.2 years ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.2 years ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74
Scholar 2.2 years ago, created an answer that has been accepted. For A: Missing SYMBOL keytype in EnsDb.Hsapiens.v75
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

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