User: deepue

gravatar for deepue
deepue130
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130
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Location:
Spain
Last seen:
1 month, 4 weeks ago
Joined:
5 years, 7 months ago
Email:
e*****************@gmail.com

Bioinformatics graduate student.

Posts by deepue

<prev • 57 results • page 1 of 6 • next >
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(Closed) How do I subset a GRanges object based on chromosome (and approximate region)?
... I have the GRanges object `data_GR`, from which I would like to extract all the regions specific to a chromosome(eg: `chr21`). How could I extract it without knowing the regions of interest? set.seed(123) data_bed = circlize::generateRandomBed(nr = 1000, nc = 0) data_GR = makeGRangesF ...
R granges written 8 weeks ago by deepue130
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biomaRt search for a list of values [dplyr + column(s)]
... Hello, I would like to query biomaRt databases for retrieving Ensembl Gene IDs (`ensembl_gene_stable_id`) for a list of SNPs (`snp_filter`) from the user input `testData$rsNum` in a *tidyverse* way. testData <- readr::read_tsv("rs1467475747 8 148357 rs1378018226 8 148383 rs546 ...
ensembl biomart written 3 months ago by deepue130 • updated 3 months ago by rpolicastro2.1k
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Comment: C: Using multiple filters in BiomaRt's getSequence
... Hi Emily, did you mean "You can <<**not**>> filter by multiple types of ID, but ..." ? ...
written 3 months ago by deepue130
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How to extract disease state of all samples from an experiment?
... Is there any packages available to extract the disease state of each sample present in an ArrayExpress experiment? ...
arrayexpress microarray R written 2.8 years ago by deepue130 • updated 2.7 years ago by Biostar ♦♦ 20
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Mapping between two affymetrix arrays
... I used to extract mappings between gene and probeset using Biomart database. Is there any way to extract mappings of probeset ids between two arrays(eg: HG-U133_Plus_2, HuGene-1_0-st-v1) ? ...
ensembl biomart mapping affymetrix written 4.0 years ago by deepue130
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Answer: A: Problem with ArrayExpress() command. Please help ..
... I have faced the below error when tried to download the experiment. Error in `row.names<-.data.frame`(`*tmp*`, value = c("E-UMCU-11_161_Measured1.txt", : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ‘E-UMCU-11 ...
written 4.1 years ago by deepue130
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Answer: A: Affy old package installation in R
... Try installing the older version of Bioconductor using install.packages("BiocInstaller", repos="http://bioconductor.org/packages/2.12/bioc") follwed by installing the `affy` package. ...
written 4.1 years ago by deepue130
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Answer: A: Masters in bioinformatics
... Some of the best universities: SASTRA University, University of Pune, Pondicherry University ...
written 4.1 years ago by deepue130
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Comment: C: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... Hi, I am still facing the issue > listMarts() Extra content at the end of the document Error: 1: Extra content at the end of the document ...
written 4.2 years ago by deepue130
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Comment: C: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... @Ben are you still looking into the issue ? Though it is around one day for the normal access, it will be useful to follow the workaround during future outages. ...
written 4.2 years ago by deepue130

Latest awards to deepue

Popular Question 7 months ago, created a question with more than 1,000 views. For compare two ped files with different number of snp information
Appreciated 19 months ago, created a post with more than 5 votes. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Great Question 19 months ago, created a question with more than 5,000 views. For BWA alignment using paired end reads from different lanes
Popular Question 19 months ago, created a question with more than 1,000 views. For pairwiseAlignment in R
Popular Question 19 months ago, created a question with more than 1,000 views. For compare two ped files with different number of snp information
Epic Question 19 months ago, created a question with more than 10,000 views. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Association analysis of big-data in R/PLINK
Popular Question 2.4 years ago, created a question with more than 1,000 views. For compare two ped files with different number of snp information
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Association analysis of big-data in R/PLINK
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to use the the filters created from VariantFiltration while using Annovar?
Great Question 3.2 years ago, created a question with more than 5,000 views. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Association analysis of big-data in R/PLINK
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How to use the the filters created from VariantFiltration while using Annovar?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How to use the the filters created from VariantFiltration while using Annovar?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 3.9 years ago, created a question with more than 1,000 views. For BWA alignment using paired end reads from different lanes
Student 3.9 years ago, asked a question with at least 3 up-votes. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Popular Question 4.3 years ago, created a question with more than 1,000 views. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Popular Question 4.6 years ago, created a question with more than 1,000 views. For BWA alignment using paired end reads from different lanes
Supporter 5.2 years ago, voted at least 25 times.

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