User: piyushjo

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piyushjo550
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Posts by piyushjo

<prev • 146 results • page 1 of 15 • next >
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Comment: C: Is Pseudotime analysis most applicable to time-series experiments?
... A single time point sample can also have cells from different developmental stages. For example, if you have sample of brain and you dissected region including SVZ to cortical layer, you will have the developmental stages a cell will pass through its differentiation gene. In that case a trajectory a ...
written 4 months ago by piyushjo550
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Comment: C: Advice for a start in Bioinformatics
... Google is your friend, unless you prefer bing. ...
written 5 months ago by piyushjo550
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Comment: C: principal component analysis (PCA) of single cell samples which come from differ
... It is correct that any integration method will forcefully correct the difference across population, as the intended function is to correct the "batch" effect here the "batch" effect are coming from disease. In the present scenario, where there are samples based on treatment (healthy vs patient) co ...
written 5 months ago by piyushjo550
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Answer: A: pre-mRNA GTF reference for 10x
... Cellranger has [tutorial][1] how to make Cellranger compliant gtf from your choice of .gtf. They also mention how to convert it into premRNA gtf. I would like to tell you that in pre-mRNA gtf, genes that are overlapped by other genes will not be counted. For that, you should align the reads to exo ...
written 5 months ago by piyushjo550
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Answer: A: principal component analysis (PCA) of single cell samples which come from differ
... I will suggest using [FastMNN()][1] wrapper, also available with Seurat package, to integrate different samples. CCA, in my and others' experience performs forceful integration. It is useful only if you know all the libraries are biological/technical replicates. [1]: https://github.com/satijala ...
written 5 months ago by piyushjo550
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Comment: C: Compare signatures between scRNA-seq clusters in R
... > However, as I understood, these score values should not be compared > between the different signatures because they do not have a "physical > meaning" This statement says that you cannot compare between two signatures, but you can still compare between clusters. For example the cell cyc ...
written 5 months ago by piyushjo550
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Comment: C: Tophat / output without XS
... Is this RNA-seq data? Any particular reason you are using tophat and not new aligners like HISAT2 or STAR? In HISAT2 you have to specify strandness, in default condition it assumes unstranded, could be the same issue with tophat. ...
written 5 months ago by piyushjo550
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Comment: C: Recommendation for packages for cell type deconvolution from bulk RNAseq data?
... I have also used GSVA and found it to be really easy and good. Below paper also performed a comparison where GSVA was recommended, you can read for more details. One of the way one colleague of mine has done is to combine GSVA enrichment score with gene correlation score. For correlation, you can ...
written 5 months ago by piyushjo550
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Comment: C: What are the benefits of using Linux system for Bioinformatics?
... As my friend says, Because Yes :D In reality, a lot of programs are made to run on Linux and Mac, and sometimes only Linux. While Mac is expensive (and really expensive), Linux is free, you have freedom for different distros, plus the online community can solve all your problems. I never really tri ...
written 5 months ago by piyushjo550
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Comment: C: PCA on FPKM data
... It's alright. You are the pro! I was just trying to get more information but you had better answer. ...
written 5 months ago by piyushjo550

Latest awards to piyushjo

Popular Question 18 days ago, created a question with more than 1,000 views. For RNA-strandness of single cell library prep methods
Popular Question 11 weeks ago, created a question with more than 1,000 views. For gffread conversion leaves gene_id
Popular Question 3 months ago, created a question with more than 1,000 views. For gffread conversion leaves gene_id
Great Question 3 months ago, created a question with more than 5,000 views. For How different is rlog transformation from vst transformation in DESeq2
Popular Question 4 months ago, created a question with more than 1,000 views. For gffread conversion leaves gene_id
Popular Question 4 months ago, created a question with more than 1,000 views. For what is inverse normalized RNA-seq expression and how to do that?
Popular Question 4 months ago, created a question with more than 1,000 views. For what is inverse normalized RNA-seq expression and how to do that?
Popular Question 4 months ago, created a question with more than 1,000 views. For Single cell clutering after regressing out cell cycle effect using seurat
Popular Question 7 months ago, created a question with more than 1,000 views. For Creating interaction network using cytoscape
Popular Question 7 months ago, created a question with more than 1,000 views. For Hisat2 index building taking days even with 40 GB RAM
Centurion 7 months ago, created 100 posts.
Supporter 7 months ago, voted at least 25 times.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: how do I split fastq from SRA?
Popular Question 14 months ago, created a question with more than 1,000 views. For How different is rlog transformation from vst transformation in DESeq2
Scholar 14 months ago, created an answer that has been accepted. For A: Get a bunch of ENTREZID into gene symbols
Popular Question 17 months ago, created a question with more than 1,000 views. For How different is rlog transformation from vst transformation in DESeq2

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