User: Tanvir Ahamed

Reputation:
270
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Trusted
Location:
Sweden
Last seen:
2 months, 1 week ago
Joined:
3 years, 6 months ago
Email:
m********@yahoo.com

Posts by Tanvir Ahamed

<prev • 77 results • page 1 of 8 • next >
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Comment: C: how to make output plot from heatmap.2 square shaped?
... you can drag the plot window as much as u want !! ...
written 4 months ago by Tanvir Ahamed 270
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Comment: C: How to cluster single cell data using list of markers?
... You can try [SEURAT][1] , [MONOCLE][2]. There could be much more [awesome-single-cell][3] [1]: http://satijalab.org/seurat/ [2]: http://cole-trapnell-lab.github.io/monocle-release/ [3]: https://github.com/seandavi/awesome-single-cell ...
written 4 months ago by Tanvir Ahamed 270
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Comment: C: Find Corresponding GenBank ID
... I did this as a part of one of my project. This could be helpful library("genomes") proks <- reports("prokaryotes.txt") # BioProject Accession: PRJNA312015 biopro <- proks[grep("312015",proks$`BioProject ID`),] ftp_biopro <- biopro$`FTP Path` file_ty ...
written 4 months ago by Tanvir Ahamed 270
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Convert "minfi::RGChannelSet" class from OLD to NEW
... Hi, "RGChannelSet" is a class of data in minfi package. Very recently "SummarizedExperiment" package has change their class definition and so "RGChannelSet" has changed as "RGChannelSet" class is dependent on "SummarizedExperiment". Now I have saved a data in "RGChannelSet" class and I have los ...
rgchannelset minfi summarizedexperiment written 6 months ago by Tanvir Ahamed 270
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Read .eds formated file form QuantStudio 12K Flex Software in R
... I want to read data in R form QuantStudio™ 12K Flex Software which is .eds format. Can any one please suggest any package/code for this ? ...
R bioconductor quantstudio .eds written 21 months ago by Tanvir Ahamed 270
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Answer: A: Compare control probe in 450k and EPIC
... I have found [ENmix][1] package in bioconductor is very helpful regarding this issue. Helpful readings: [Innium® HD Assay Methylation Protocol Guide][2] [1]: https://www.bioconductor.org/packages/release/bioc/html/ENmix.html [2]: http://support.illumina.com/content/dam/illumina-support/docu ...
written 2.0 years ago by Tanvir Ahamed 270
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(Closed) Compare control probe in 450k and EPIC
... Based on similar sample, how to compare the control probe in 450k ad EPIC ? Any help will be appreciated . ...
450k epic written 2.0 years ago by Tanvir Ahamed 270 • updated 2.0 years ago by Charles Warden5.1k
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Comment: C: Compare 450k with EPIC
... Thanks for your suggestion . Can you please tell me, it it possible to get the same result (equivalent value) for intensity on common probe for 450k and EPIC. So for that, can i compare raw data or any further normalization or other procedure if required ? ...
written 2.1 years ago by Tanvir Ahamed 270
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Compare 450k with EPIC
... I have the idat file form a same sample in 450k and EPIC. What is the best way to compare those results? Can i compare raw data or should I apply any specific normalization before comparison? ...
450k methylation 850k epic written 2.1 years ago by Tanvir Ahamed 270 • updated 14 months ago by joshmoss110
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Comment: C: Map ensembl gene id form hg38 in hg19
... Thanks your your time and reply. I have also tried with GTF files from Ensembl FTP for both GRCh37, GRCh38 and tried to map ENSG ID from GRCh38 in GRCh37 for miRNA (BioType). But could not figured out an active solution. :( ...
written 2.1 years ago by Tanvir Ahamed 270

Latest awards to Tanvir Ahamed

Popular Question 6 months ago, created a question with more than 1,000 views. For Compare control probe in 450k and EPIC
Popular Question 6 months ago, created a question with more than 1,000 views. For Map ensembl gene id form hg38 in hg19
Popular Question 8 months ago, created a question with more than 1,000 views. For Missing value imputation for beta values of Methylation data
Popular Question 8 months ago, created a question with more than 1,000 views. For Relation between "MAPINFO" and "UCSC_CpG_Islands_Name" in Illumina manifest file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Frequency of a unique sequence in a fasta file
Popular Question 13 months ago, created a question with more than 1,000 views. For Interpretation of Beta values : Methylation data
Popular Question 15 months ago, created a question with more than 1,000 views. For Interpretation of Beta values : Methylation data
Popular Question 15 months ago, created a question with more than 1,000 views. For Relation between "MAPINFO" and "UCSC_CpG_Islands_Name" in Illumina manifest file
Popular Question 16 months ago, created a question with more than 1,000 views. For Compare 450k with EPIC
Popular Question 16 months ago, created a question with more than 1,000 views. For Interpretation of Beta values : Methylation data
Great Question 17 months ago, created a question with more than 5,000 views. For Extract sequence with header from a fasta file with specific ID given in another file
Appreciated 20 months ago, created a post with more than 5 votes. For A: How can I BLAST 4,54,871 sequences?
Supporter 2.3 years ago, voted at least 25 times.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Frequency of a unique sequence in a fasta file
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Extract sequence with header from a fasta file with specific ID given in another file
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Extract sequence with header from a fasta file with specific ID given in another file
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Frequency of a unique sequence in a fasta file
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Frequency of a unique sequence in a fasta file
Scholar 3.4 years ago, created an answer that has been accepted. For A: Extract sequence with header from a fasta file with specific ID given in another
Scholar 3.4 years ago, created an answer that has been accepted. For A: Extract sequence with header from a fasta file with specific ID given in another

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