User: enricoferrero

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enricoferrero740
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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 8 days ago by enricoferrero740 • updated 7 days ago by Kevin Blighe25k
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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 15 months ago by enricoferrero740
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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 15 months ago by enricoferrero740
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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 15 months ago by enricoferrero740 • updated 15 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 22 months ago by enricoferrero740
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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 23 months ago by enricoferrero740
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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 24 months ago by enricoferrero740
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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 24 months ago by enricoferrero740
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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 2.0 years ago by enricoferrero740
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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 3.2 years ago by enricoferrero740 • updated 13 months ago by hongbo91920

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Great Question 15 months ago, created a question with more than 5,000 views. For Remove Illumina TruSeq Index adapters
Great Question 15 months ago, created a question with more than 5,000 views. For Best Tools For Motif Finding And/Or De Novo Motif Discovery?
Great Question 15 months ago, created a question with more than 5,000 views. For Retrieve All Genes Associated With A Go Term
Epic Question 15 months ago, created a question with more than 10,000 views. For Retrieve All Genes Associated With A Go Term
Epic Question 15 months ago, created a question with more than 10,000 views. For Remove mitochondrial reads from BAM files
Popular Question 15 months ago, created a question with more than 1,000 views. For Differential Methylation Analysis
Popular Question 15 months ago, created a question with more than 1,000 views. For Remove Illumina TruSeq Index adapters
Student 15 months ago, asked a question with at least 3 up-votes. For Remove Illumina TruSeq Index adapters
Great Question 20 months ago, created a question with more than 5,000 views. For Remove mitochondrial reads from BAM files
Student 20 months ago, asked a question with at least 3 up-votes. For I Work A Lot With Table-Like Structures, Should I Learn Sql?
Popular Question 20 months ago, created a question with more than 1,000 views. For Select Nearest Neighbors Shared By More Than One Selected Node
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Good Question 2.4 years ago, asked a question that was upvoted at least 5 times. For Retrieve All Genes Associated With A Go Term
Popular Question 2.4 years ago, created a question with more than 1,000 views. For I Work A Lot With Table-Like Structures, Should I Learn Sql?
Great Question 2.7 years ago, created a question with more than 5,000 views. For Retrieve All Genes Associated With A Go Term
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Select Nearest Neighbors Shared By More Than One Selected Node
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Transcription Factors <--> Regulated Genes Database
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Resources For Ngs?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Transcription Factors <--> Regulated Genes Database
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