User: enricoferrero

gravatar for enricoferrero
enricoferrero740
Reputation:
740
Status:
Trusted
Location:
United Kingdom
Last seen:
9 months, 1 week ago
Joined:
5 years, 7 months ago
Email:
e**************@gmail.com

Posts by enricoferrero

<prev • 64 results • page 1 of 7 • next >
0
votes
1
answer
361
views
1
answers
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 9 months ago by enricoferrero740
0
votes
1
answer
361
views
1
answers
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 9 months ago by enricoferrero740
2
votes
1
answer
361
views
1
answer
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 9 months ago by enricoferrero740 • updated 9 months ago by Lars Juhl Jensen11k
0
votes
0
answers
616
views
0
answers
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 16 months ago by enricoferrero740
0
votes
3
answers
964
views
3
answers
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 17 months ago by enricoferrero740
0
votes
3
answers
964
views
3
answers
Comment: C: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... All right, no worries - I can wait till Tuesday ;) ...
written 18 months ago by enricoferrero740
0
votes
3
answers
964
views
3
answers
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 18 months ago by enricoferrero740
0
votes
0
answers
478
views
0
answers
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 18 months ago by enricoferrero740
3
votes
2
answers
1.8k
views
2
answers
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 2.7 years ago by enricoferrero740 • updated 7 months ago by hongbo91920
28
votes
6
answers
9.2k
views
12 follow
6
answers
Remove mitochondrial reads from BAM files
... 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! ...
bam samtools rna-seq awk written 3.1 years ago by enricoferrero740 • updated 4 months ago by Simply Bioinformatics70

Latest awards to enricoferrero

Great Question 14 months ago, created a question with more than 5,000 views. For Remove mitochondrial reads from BAM files
Student 14 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 14 months ago, created a question with more than 1,000 views. For Select Nearest Neighbors Shared By More Than One Selected Node
Popular Question 15 months ago, created a question with more than 1,000 views. For Select Nearest Neighbors Shared By More Than One Selected Node
Popular Question 16 months ago, created a question with more than 1,000 views. For Select Nearest Neighbors Shared By More Than One Selected Node
Voter 18 months ago, voted more than 100 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For Best Tools For Motif Finding And/Or De Novo Motif Discovery?
Appreciated 22 months ago, created a post with more than 5 votes. For I Work A Lot With Table-Like Structures, Should I Learn Sql?
Good Question 22 months ago, asked a question that was upvoted at least 5 times. For Retrieve All Genes Associated With A Go Term
Popular Question 22 months 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 2.2 years ago, created a question with more than 5,000 views. For Retrieve All Genes Associated With A Go Term
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Select Nearest Neighbors Shared By More Than One Selected Node
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Transcription Factors <--> Regulated Genes Database
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Resources For Ngs?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Transcription Factors <--> Regulated Genes Database
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Best Tools For Motif Finding And/Or De Novo Motif Discovery?
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 I Work A Lot With Table-Like Structures, Should I Learn Sql?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Transcription Factors <--> Regulated Genes Database
Popular Question 2.9 years ago, created a question with more than 1,000 views. For I Work A Lot With Table-Like Structures, Should I Learn Sql?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Transcription Factors <--> Regulated Genes Database
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Transcription Factors <--> Regulated Genes Database
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Best Tools For Motif Finding And/Or De Novo Motif Discovery?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Best Way To Visualize Geneontology Enrichments For Multiple Datasets?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Transcription Factors <--> Regulated Genes Database

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 514 users visited in the last hour