User: Ar

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Ar890
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890
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aayushraman
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4 weeks, 1 day ago
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4 years, 2 months ago
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Posts by Ar

<prev • 81 results • page 1 of 9 • next >
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Comment: C: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
... `` It is not like, the input control or IgG control for ChIP. Then do you think I should still include them for learning the model? `` You can include them but a lot of your called by ChromHMM or MACS would have false positives. Ideally, it should be a whole genome input control or IgG-treated file. ...
written 5 weeks ago by Ar890
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Answer: A: WGCNA cannot be done to compare two conditions?
... I believe it is not the condition but the number of replicates that are required for running WGCNA. Typically, you are required to have more than 15 samples. Ideally, I would recommend more than 30 replicates for each condition. Here is the list of frequently asked questions: https://horvath.genet ...
written 5 weeks ago by Ar890
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Answer: A: Questions related to ChromHMM+using MACS2 peak calling output bed file as input
... Here are the answers to your questions: 1. Don't merge and run all of them together. 2. One of the first steps of ChromHMM is peak calling. Therefore, you need to use the bed files from bam files and not peak files. Although the default settings (i.e. ) would give you less stringent calls (argumen ...
written 5 weeks ago by Ar890
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Tool: DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
... **Update**: Our manuscript has been published in Bioinformatics -- https://doi.org/10.1093/bioinformatics/btx635. **Abstract**: We propose a data-adaptive, non-parametric, and non-regression approach to remove the biological signal to prepare the data for batch detection and then apply a semi-NMF ...
scrna-seq R batcheffects tool rna-seq written 2.1 years ago by Ar890
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Comment: C: ComBat (SVA) Application - Two Technical Effects
... I am sorry but for some reason the post came up on the "Biostars Latest question". I think it was because the Biostar modified your post. However, thanks for sending the paper. I will go through it. ...
written 2.8 years ago by Ar890
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Comment: C: ComBat (SVA) Application - Two Technical Effects
... Here is my earlier post on Batch Correction: https://www.biostars.org/p/196430/#196528 I would recommend you to combine all the dataset you have and then get the batch information using sva function. Now sva gives you surrogate variables (which is batch plus information about other latent variables ...
written 2.8 years ago by Ar890
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DESeq2 design and interaction terms
... I went through the vignette about interaction terms and would like to understand if I am applying interaction terms correctly and biologically, if I am extracting the correct the terms. Here is the example code from DESeq2 R documentation for **two conditions (A, B) and three genotypes (I,II,III)**. ...
R deseq2 rna-seq written 2.9 years ago by Ar890
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Answer: A: PCA tpm fpkm
... I would recommend to do log-transformation of the TPM/RSEM dataset. PCA has a hidden assumption of normality. PCA finds the coordinate system such that it can maximize the variance between the points. This achieved using orthogonal principal components. In case of multivariate Gaussian distribution ...
written 2.9 years ago by Ar890
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Thanks and that was an awesome answer! Actually you made my stupid question look good! :D ...
written 2.9 years ago by Ar890
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
... Thanks a lot. That was helpful! ...
written 2.9 years ago by Ar890

Latest awards to Ar

Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Appreciated 11 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Good Question 11 months ago, asked a question that was upvoted at least 5 times. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Popular Question 11 months ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Appreciated 12 months ago, created a post with more than 5 votes. For A: Beginner in Bioinformatics / computational biology field
Popular Question 16 months ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Scholar 16 months ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Popular Question 17 months ago, created a question with more than 1,000 views. For List of genes expressed in Brain and different tissues
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Popular Question 23 months ago, created a question with more than 1,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Student 2.6 years ago, asked a question with at least 3 up-votes. For Difference between the Fasta files from UCSC and Gencode/Ensembl
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Supporter 3.1 years ago, voted at least 25 times.
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Limma strange low p-values.
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Beginner in Bioinformatics / computational biology field
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?
Scholar 3.1 years ago, created an answer that has been accepted. For A: Public paired end chip seq dataset, both ChIP and input?

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