User: enricoferrero
enricoferrero • 740
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Posts by enricoferrero
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... Can you please point me to the method you used to map these IDs to SMILES? Thanks ...
written 13 months ago by
enricoferrero • 740
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... And yet on LIFE I can see BRD to PubChem IDs mappings so it must be possible to do that (without having to go through SMILES):
![enter image description here][1]
[1]: http://imgur.com/download/7UZEN8v ...
written 13 months ago by
enricoferrero • 740
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... I have some IDs from LINCS/CMap (e.g.: BRD-A00267231) that I need to convert to either ChEMBL or PubChem IDs.
I usually use [UniChem][1] for this kind of stuff but BRD identifiers are not recognised.
BRD identifiers are used in most (all?) LINCS resources such as [clue.io][2], [Harmonizome][3], [L1 ...
written 13 months ago by
enricoferrero • 740
• updated
13 months ago by
Lars Juhl Jensen ♦ 11k
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... Hello,
I'm trying to perform an analysis similar to those in ENCODE or FANTOM publications where enrichment of GWAS SNPs in regulatory regions (e.g.: DHSs, CAGE-defined enhancers) is calculated (1,2).
So, I would like to calculate if a set of GWAS SNPs associated with a disease of interest is enri ...
written 20 months ago by
enricoferrero • 740
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... Just to report I'm still getting errors using biomaRt through R, with both the main server and a mirror:
> ensembl <- useMart("ensembl", "hsapiens_gene_ensembl")
Extra content at the end of the document
Error: 1: Extra content at the end of the document
> ensembl <- useM ...
written 21 months ago by
enricoferrero • 740
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... All right, no worries - I can wait till Tuesday ;) ...
written 21 months ago by
enricoferrero • 740
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... Still having issues here:
> ensembl <- useMart("ensembl", "hsapiens_gene_ensembl", host="useastdb.ensembl.org", port=3306)
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http: ...
written 21 months ago by
enricoferrero • 740
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... Hello,
I'm looking for tools that allow identification of active modules in networks.
A typical scenario is where you have a protein-protein interaction network and some gene expression data overlaid on top of it and you want to identify set of connected nodes in the network that show significant ...
written 21 months ago by
enricoferrero • 740
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... Hi,
I've just started working in this area and am looking for some pointers.
What software packages does the community use for the analysis of differentially methylated regions from WGBS data?
I used Bismark to perform the alignment and the methylation calling steps.
Thanks!
...
written 3.0 years ago by
enricoferrero • 740
• updated
10 months ago by
hongbo919 • 20
29
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12 follow
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... Hi,
I have a somewhat high content of mitochondrial RNA in my RNA-seq experiment. Is there a way to use samtools to remove alignments to the 'MT' chromosome and keep all the rest?
I'm considering using samtools view in combination with awk but perhaps there's a better/cleaner solution?
Thanks!
...
written 3.3 years ago by
enricoferrero • 740
• updated
7 months ago by
Simply Bioinformatics • 80
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