User: Ar
Ar • 930
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Posts by Ar
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... Hello Everyone,
I am having issues with demultiplexing a publically available dataset on SRA (https://www.ncbi.nlm.nih.gov/sra/SRX4061030). It is a single-cell inDrop dataset and would like to know what is the best way to demultiplex it.
Any advice or help would be appreciated.
Thanks! ...
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... ``
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 8 months ago by
Ar • 930
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... 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 8 months ago by
Ar • 930
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... 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 8 months ago by
Ar • 930
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... **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 ...
written 2.7 years ago by
Ar • 930
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... 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 3.4 years ago by
Ar • 930
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... 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 3.4 years ago by
Ar • 930
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... 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)**. ...
written 3.5 years ago by
Ar • 930
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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 3.5 years ago by
Ar • 930
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... Thanks and that was an awesome answer! Actually you made my stupid question look good! :D ...
written 3.5 years ago by
Ar • 930
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For DESeq2 design and interaction terms
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For Difference between the Fasta files from UCSC and Gencode/Ensembl
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