User: enricoferrero

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enricoferrero750
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Posts by enricoferrero

<prev • 65 results • page 1 of 7 • next >
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Resources for machine learning prediction of phenotypes from omics data
... Hello, I'm looking for resources (reviews, papers, tutorials) on using machine learning approaches that discriminate between phenotypic or clinical characteristics using omics data as input. Simplest case scenario would be to build a classifier on gene expression profiles of patients with or witho ...
omics gene expression machine learning written 4 months ago by enricoferrero750 • updated 4 months ago by Kevin Blighe33k
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Comment: C: How do I convert LINCS/CMap IDs to ChEMBL/PubChem IDs?
... Can you please point me to the method you used to map these IDs to SMILES? Thanks ...
written 19 months ago by enricoferrero750
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Comment: C: How do I convert LINCS/CMap IDs to ChEMBL/PubChem IDs?
... 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 19 months ago by enricoferrero750
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How do I convert LINCS/CMap IDs to ChEMBL/PubChem IDs?
... 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 ...
pubchem unichem chembl lincs cmap written 19 months ago by enricoferrero750 • updated 19 months ago by Lars Juhl Jensen11k
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Enrichment of GWAS SNPs in regulatory regions
... 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 ...
enrichment fisher gwas written 2.2 years ago by enricoferrero750
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Comment: C: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... 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 2.3 years ago by enricoferrero750
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Comment: C: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... All right, no worries - I can wait till Tuesday ;) ...
written 2.3 years ago by enricoferrero750
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Comment: C: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... 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 2.3 years ago by enricoferrero750
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Tools for network active module identification?
... 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 ...
R network jactivemodules bioconductor cytoscape written 2.3 years ago by enricoferrero750
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Differential Methylation Analysis
... 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! ...
methylation wgbs written 3.5 years ago by enricoferrero750 • updated 17 months ago by hongbo91920

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