User: deepue

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deepue130
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130
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Location:
Finland
Last seen:
4 months ago
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5 years, 3 months ago
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Bioinformatics graduate student.

Posts by deepue

<prev • 54 results • page 1 of 6 • next >
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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 2.5 years ago by deepue130 • updated 2.4 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 3.7 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 3.8 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 3.8 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 3.8 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 3.9 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 3.9 years ago by deepue130
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Answer: A: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... Is there any option of using Ensembl through biomaRt package ? At the moment, I am not able to access the marts. ...
written 3.9 years ago by deepue130
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How to extract organism information from the Expression Atlas experiments using SPARQL queries
... I have been extracting the list of experiments from Expression Atlas with accession numbers, platform information using the below query. query <- "PREFIX rdf: PREFIX rdfs: PREFIX dcterms: PREFIX atlasterms: SELECT DISTINCT ?experiment ?accession ?description ?platfor ...
rdf sparql expressionatlas R written 4.1 years ago by deepue130
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caret svm for precomputed kernels
... Hi, Is there any possibility of using precomputed kernels in caret package's SVM function ? It can be used in kernlab's ksvm function but the algorithm is very slow compared to parallel processing of caret's functions. ...
R svm kernels caret written 4.1 years ago by deepue130

Latest awards to deepue

Appreciated 15 months ago, created a post with more than 5 votes. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Great Question 15 months ago, created a question with more than 5,000 views. For BWA alignment using paired end reads from different lanes
Popular Question 15 months ago, created a question with more than 1,000 views. For pairwiseAlignment in R
Popular Question 15 months ago, created a question with more than 1,000 views. For compare two ped files with different number of snp information
Epic Question 15 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 2.1 years ago, created a question with more than 1,000 views. For Association analysis of big-data in R/PLINK
Popular Question 2.1 years ago, created a question with more than 1,000 views. For compare two ped files with different number of snp information
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Association analysis of big-data in R/PLINK
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 2.5 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 2.9 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 2.9 years ago, created a question with more than 1,000 views. For Association analysis of big-data in R/PLINK
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 2.9 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 3.1 years ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 3.1 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 3.6 years ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 3.6 years ago, created a question with more than 1,000 views. For BWA alignment using paired end reads from different lanes
Student 3.6 years ago, asked a question with at least 3 up-votes. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Teacher 3.9 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 4.0 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 4.1 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 4.3 years ago, created a question with more than 1,000 views. For BWA alignment using paired end reads from different lanes
Supporter 4.9 years ago, voted at least 25 times.

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