User: enricoferrero

gravatar for enricoferrero
enricoferrero560
Reputation:
560
Status:
Trusted
Location:
United Kingdom
Last seen:
1 month ago
Joined:
4 years, 10 months ago
Email:
e**************@gmail.com

Posts by enricoferrero

<prev • 124 results • page 1 of 13 • next >
0
votes
0
answers
779
views
0
answers
Comment: C: Invitation to submit articles to the Bioconductor gateway on F1000Research
... I have a cross-package workflow which was approved by referees a few weeks ago: https://f1000research.com/articles/7-121/v2 I would love for it to be part of BioC 2018 - is that possible even if it was published before the call? ...
written 5 weeks ago by enricoferrero560
0
votes
0
answers
132
views
0
answers
Comment: C: Gviz IdeogramTrack fails with Error: failed to load HTTP resource
... This might be related to https://support.bioconductor.org/p/105322/ though the error message appears to be different. ...
written 3 months ago by enricoferrero560
0
votes
0
answers
132
views
0
answers
Gviz IdeogramTrack fails with Error: failed to load HTTP resource
... Hello, I get an HTTP connection error when using Gviz::IdeogramTrack(): library(Gviz) IdeogramTrack(genome="hg19", chromosome="chr7") Error: failed to load HTTP resource traceback() 18: stop(e) 17: (function (msg, code, domain, line, col, level, filename, class = "XMLError") { e = m ...
rtracklayer gviz http gviz-package written 3 months ago by enricoferrero560
0
votes
1
answers
150
views
1
answers
Comment: C: [VariantAnnotation] Preserve query metadata with locateVariants()
... Thanks Valerie, it works perfectly - not sure how I missed that column in the results object! ...
written 5 months ago by enricoferrero560
2
votes
1
answer
150
views
1
answer
[VariantAnnotation] Preserve query metadata with locateVariants()
... Is there any way to preserve the metadata in the query GRanges object when using locateVariants(query, subject, AllVariants()) from VariantAnnotation? Or is it possible to add the query metadata to the resulting GRanges? When calculating overlaps between two GRanges object I usually use findOverla ...
variantannotation metadata locatevariants mcols written 5 months ago by enricoferrero560 • updated 5 months ago by Valerie Obenchain ♦♦ 6.5k
0
votes
2
answers
249
views
2
answers
Answer: A: [gwascat] Updated GWAS catalog from file
... Based on Robert Castelo's answer below, I ended up doing this: download.file("http://www.ebi.ac.uk/gwas/api/search/downloads/alternative", destfile = "gwas_catalog_v1.0.1-associations_e90_r2017-12-04.tsv") snps <- read.delim("gwas_catalog_v1.0.1-associations_e90_r2017-12-04.tsv", check.names = ...
written 5 months ago by enricoferrero560
0
votes
2
answers
249
views
2
answers
Comment: C: [gwascat] Updated GWAS catalog from file
... Thanks. Yes, this would probably work but it's not very elegant - especially considering this is training material for students. I wonder wheter it would not be easier and more straightforward to follow to simply create a GRanges object at that point? ...
written 5 months ago by enricoferrero560
4
votes
2
answers
249
views
2
answers
[gwascat] Updated GWAS catalog from file
... Hello, Is there any way to get an up-to-date version of the GWAS catalog starting from an existing file? Currently the version accessible with data(ebicat38) is outdated (January 2016) and the function makeCurrentGwascat() only accepts a URL as argument, not an existing file. I'm preparing some tr ...
gwascat written 5 months ago by enricoferrero560
0
votes
2
answers
376
views
2
answers
Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... Yep, this solves it, thank you. Feel free to add it as an answer so I can accept it. ...
written 12 months ago by enricoferrero560
0
votes
2
answers
376
views
2
answers
Comment: C: keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
... This is cool but, is there a way to grab the EnsDb object without having to look up its name in the AnnotationHub (i.e.:  AH53211)? BTW, I didn't mean to hijack my own thread : i still get that error when trying to access the EnsDb objects with keys() or genes(). ...
written 12 months ago by enricoferrero560

Latest awards to enricoferrero

Popular Question 12 months ago, created a question with more than 1,000 views. For [DESeq2] Cook's distance flagging for continuous variables
Popular Question 12 months ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Popular Question 12 months ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
Great Question 12 months ago, created a question with more than 5,000 views. For How to properly sort GRanges?
Great Question 12 months ago, created a question with more than 5,000 views. For [GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
Popular Question 12 months ago, created a question with more than 1,000 views. For biomaRt proxy issues
Scholar 12 months ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Student 13 months ago, asked a question with at least 3 up-votes. For Can't upgrade to Bioconductor 3.3?
Popular Question 13 months ago, created a question with more than 1,000 views. For biomaRt proxy issues
Popular Question 2.1 years ago, created a question with more than 1,000 views. For [DESeq2] Cook's distance flagging for continuous variables
Scholar 2.1 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Centurion 2.1 years ago, created 100 posts.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Linkage disequilibrium with 1000 Genomes/HapMap
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Simple pathway enrichment analysis for gene lists
Popular Question 2.1 years ago, created a question with more than 1,000 views. For biomaRt proxy issues
Scholar 2.1 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For biomaRt no longer works with proxy after upgrade
Popular Question 2.3 years ago, created a question with more than 1,000 views. For biomaRt no longer works with proxy after upgrade
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to properly sort GRanges?
Scholar 2.5 years ago, created an answer that has been accepted. For A: How to correctly import Bismark coverage files into bsseq?
Supporter 2.5 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 424 users visited in the last hour