User: deepue

gravatar for deepue
deepue110
Reputation:
110
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Location:
Finland
Last seen:
1 day, 8 hours ago
Joined:
3 years, 2 months ago
Email:
e*****************@gmail.com

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 5 months ago by deepue110 • updated 3 months 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 20 months ago by deepue110
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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 20 months ago by deepue110
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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 20 months ago by deepue110
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Answer: A: Masters in bioinformatics
... Some of the best universities: SASTRA University, University of Pune, Pondicherry University ...
written 21 months ago by deepue110
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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 21 months ago by deepue110
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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 21 months ago by deepue110
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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 22 months ago by deepue110
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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 2.0 years ago by deepue110
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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 2.1 years ago by deepue110

Latest awards to deepue

Popular Question 5 months ago, created a question with more than 1,000 views. For Association analysis of big-data in R/PLINK
Popular Question 5 months ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 5 months 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 10 months ago, created a question with more than 5,000 views. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Popular Question 10 months ago, created a question with more than 1,000 views. For Association analysis of big-data in R/PLINK
Popular Question 10 months ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 10 months 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 12 months ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 12 months 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 18 months ago, created a question with more than 1,000 views. For Plink extract SNPs from .ped file using ID
Popular Question 18 months ago, created a question with more than 1,000 views. For BWA alignment using paired end reads from different lanes
Student 18 months ago, asked a question with at least 3 up-votes. For How to identify Homozygous or Heterozygous variants from the annotation file ?
Teacher 22 months 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 24 months ago, created a question with more than 1,000 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 How to identify Homozygous or Heterozygous variants from the annotation file ?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For BWA alignment using paired end reads from different lanes
Supporter 2.8 years ago, voted at least 25 times.

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