User: gokcen.eraslan

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10
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New User
Location:
Germany
Last seen:
2 years, 8 months ago
Joined:
4 years, 3 months ago
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g*************@gmail.com

Posts by gokcen.eraslan

<prev • 8 results • page 1 of 1 • next >
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Comment: C: lpsymphony install on Ubuntu
... That fixed it for me, thanks a lot! ...
written 2.7 years ago by gokcen.eraslan10
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Comment: C: makeAttr() missing in KEGGgraph
... i.e. https://github.com/Bioconductor-mirror/KEGGgraph/blob/344179ddb8b51774819e746e3ddd38d32e07a157/vignettes/KEGGgraph.Rnw#L193 ...
written 3.2 years ago by gokcen.eraslan10
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Comment: C: Generating a proper TxDb instance from NCBI GFF Annotations File
... Thanks for the reply. Would it make sense to add resulting TxDb to Bioconductor as an official annotation package :) People do not suffer as much as I did, at least. ...
written 3.8 years ago by gokcen.eraslan10
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Comment: C: Generating a proper TxDb instance from NCBI GFF Annotations File
... Thanks for the reply. GenomeInfoDb:::fetch_assembly_report('GCF_000001405.25') retrieves and parses  ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.25.assembly.txt So RefSeqAccn and UCSCStyleName columns can be used to convert NC_ and NT_ ids to UCSC ones, but no luck for N ...
written 3.8 years ago by gokcen.eraslan10
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Comment: C: Generating a proper TxDb instance from NCBI GFF Annotations File
... Thanks for the reply. I also thought about that, but they also report hg19-based coordinates on the webpage. Is it the case that they also map new transcripts to older assemblies? ...
written 3.8 years ago by gokcen.eraslan10
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Generating a proper TxDb instance from NCBI GFF Annotations File
... I have some RefSeq transcript IDs e.g. NM_123 and NR_123 and some genomic positions from hg19 assembly. I'm trying to use the NCBI Genome Annotations in my analysis. Since I couldn't find a ready-to-use NCBI annotation TxDb file in Bioconductor, I tried to generate my own from the following GFF file ...
genomeinfodb ncbi maketxdbfromgff refseq fetchextendedchrominfofromucsc written 3.8 years ago by gokcen.eraslan10 • updated 3.8 years ago by Hervé Pagès ♦♦ 14k
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GRASP2 truncated phenotype descriptions
... Hi, I am running into truncated phenotype categories when I use GRASP2 like this: > library(grasp2db) > GRASP2() %>% tbl(., 'study') %>% filter(PaperPhenotypeDescription %like% '%cystic fibrosis%') %>% select(PaperPhenotypeDescription) %>% as.data.frame ...
annotationhub grasp2 grasp2db written 4.0 years ago by gokcen.eraslan10 • updated 4.0 years ago by Martin Morgan ♦♦ 24k
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Error in the Illumina ID to Gene Symbol mapping through lumi package
... I am using lumi package to map some Illumina probe IDs to gene symbols but I get the following output. It seems some entries are shifted somehow. Is this a bug in the package?   > probeID2nuID(c("ILMN_1798177", "ILMN_1798177", "ILMN_1753164", "ILMN_1753164"), lib.mapping = 'lumiH ...
lumi lumihumanidmapping illuminahumanv3 written 4.3 years ago by gokcen.eraslan10

Latest awards to gokcen.eraslan

Popular Question 2.7 years ago, created a question with more than 1,000 views. For Generating a proper TxDb instance from NCBI GFF Annotations File
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Error in the Illumina ID to Gene Symbol mapping through lumi package

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