User: Patrick Schorderet

Reputation:
20
Status:
New User
Location:
United States
Last seen:
2 years, 6 months ago
Joined:
4 years, 3 months ago
Email:
p*****************@molbio.mgh.harvard.edu

Posts by Patrick Schorderet

<prev • 23 results • page 1 of 3 • next >
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Comment: C: From a GRanges object to a GRangeList
... Great, that's exactly what I was looking for. Is there an easy way to use the mirna_id as names for the list elements? and do this in one go? ...
written 2.5 years ago by Patrick Schorderet20
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From a GRanges object to a GRangeList
... Hi All, I'm trying to create a GRangesList from a GRanges object. I basically have a Granges object called miRNA. It has 302 ranges. I also have a function that requires me to feed it with a GrangesList, so I am trying to alter the Granges object to a list format with each element of the list conta ...
granges grangeslist written 2.5 years ago by Patrick Schorderet20 • updated 2.5 years ago by James W. MacDonald45k
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Answer: A: select() gene in db not working although key exists
... Great, thanks a lot! ...
written 2.6 years ago by Patrick Schorderet20
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select() gene in db not working although key exists
...   Hi all, I'm trying to find the names (e.g. SYMBOLS) corresponding to gene ID using the "org.Dm.eg.db" and "TxDb.Dmelanogaster.UCSC.dm3.ensGene" libraries. I have done it (and it works) when I try with the mm9 (mouse) genome, but some how, I get an error if I try with the drosophila genome. I ha ...
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Comment: C: Genome side annotation for drosophila
... exactly, great! thanks. ...
written 2.6 years ago by Patrick Schorderet20
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Genome side annotation for drosophila
... I'm looking for a genome wide annotation for Drosophila Melanogaster in the same format and analogous to the org.Mm.eg.db. Anyone knows if this exists? ...
drosophila melanogaster org.mm.eg.db genome annotation written 2.6 years ago by Patrick Schorderet20 • updated 2.6 years ago by Marc Carlson7.2k
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Answer: A: Does BSgenome.Dmelanogaster.UCSC.dm2 maintain non-coding RNAs?
... Thanks Hervé and Johannes, Just tried to use the old function (makeTranscriptDbFromBiomart) and it looks like something is going wrong (pasting the error message below). I guess the easiest will be to wait for the new BioC update. Should this work well with the update? Thanks for the help Patrick ...
written 2.6 years ago by Patrick Schorderet20
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Comment: C: Does BSgenome.Dmelanogaster.UCSC.dm2 maintain non-coding RNAs?
...   Hey Hervé, Is the makeTxDfFromBiomart a function that only works on R 3.2? I tried and it gives me an error :-( txdb <- makeTxDbFromBiomart(dataset="dmelanogaster_gene_ensembl") Error: could not find function "makeTxDbFromBiomart" and my sessionInfo() R version 3.1.3 (2015-03-09) Platform: ...
written 2.6 years ago by Patrick Schorderet20
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Answer: A: Does BSgenome.Dmelanogaster.UCSC.dm2 maintain non-coding RNAs?
... ok, great. Thanks for this info, i'll check it out. Patrick ...
written 2.6 years ago by Patrick Schorderet20
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Comment: C: Does BSgenome.Dmelanogaster.UCSC.dm2 mountain non-coding RNAs?
... Yes, sorry, you are right. Here is what I do: I count RNAseq reads using the TxDb.Dmelanogaster.UCSC.dm3.ensGene database to compute DEGs. However, I would also be interested in looking at whether ncRNAs (lincRNAs) are up or down regulated.  I hope this makes more sense. Thanks. ...
written 2.6 years ago by Patrick Schorderet20

Latest awards to Patrick Schorderet

Popular Question 2.5 years ago, created a question with more than 1,000 views. For package ‘edgeR’ is not available (for R version 3.1.2)
Popular Question 2.5 years ago, created a question with more than 1,000 views. For package ‘edgeR’ is not available (for R version 3.1.2)

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