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User: piyushjo

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piyushjo • 100
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Posts by piyushjo

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Comparing stranded reads to unstranded reads
... Ok. Thanks. I am comparing cerebellum to medulloblastoma (cancer of cerebellum). The only thing I think bothers me is if the anti-sense transcripts for an overlapping mRNA would be improperly quantified. ...
written 3 days ago by piyushjo • 100
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Comment: C: Comparing stranded reads to unstranded reads
... But main question is just because one library is stranded and the other is unstranded, would that make them incomparable? I understand differences from human and machines are also involved. ...
written 4 days ago by piyushjo • 100
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Comment: C: Comparing stranded reads to unstranded reads
... But doesn't DESeq2 takes into account the difference in library depth? What else could be contributing to variation? ...
written 4 days ago by piyushjo • 100
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Comparing stranded reads to unstranded reads
... Hi, I have two datasets from different sources. Unfortunately one group have done unstranded RNA-seq while the second one has done stranded. When I do the PCA analysis of normalized reads using DESeq2, I see them clustering far from each other. Now I am doubtful if there is an artefact coming from ...
de gene strand information rna-seq written 4 days ago by piyushjo • 100 • updated 4 days ago by johnsonnathant • 70
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Comment: C: Tips for network prediction: WGCNA vs ARACNE (or MINET)
... Hi Fuyingxue, Thanks for your input and sharing the review article. ...
written 11 days ago by piyushjo • 100
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Comment: C: RNA-strandness of single cell library prep methods
... Sorry! I used the imagedb website. ...
written 23 days ago by piyushjo • 100
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Comment: C: Creating interaction network using cytoscape
... Hi karthic. I am interested in using the microarray data to build PPI or transcriptional inference network. The ClusterOne app uses Mass Spec data. ...
written 25 days ago by piyushjo • 100
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Need help understanding ARACNe-AP output
... Hi, I have used java based ARACNe-AP to find interaction partners of genes involved in metabolic pathway of my interest. I have data (65 samples) from tumor and matched samples. I want to understand what are novel interactions present in tumor environment. When I run the program, I get a list of "R ...
ppi network aracne written 25 days ago by piyushjo • 100
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Creating interaction network using cytoscape
... Hi, I have expression data from 65 patient. I am interested in creating protein-protein interaction network based on known interaction (STRINGdb) and expression (RNA-seq). My main purpose is to identify what interactions are present in tumor vs normal cell, as I have expression data for both. I am ...
ppi expression data cytoscape written 4 weeks ago by piyushjo • 100 • updated 4 weeks ago by scooter • 70
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Answer: A: How to retrieve sets of protein sequences?
... Ensembl biomart. It takes any sort of id: Refseq, HGNC, or just gene name. http://useast.ensembl.org/biomart/martview/bfc7092adedc70231fd4027a5b8eaaed 1) Choose data set (Ensembl v94) 2) Filters: Gene name, ensemble id, refseq id or anything 3) Attributes: In features choose "gene id" or "gene na ...
written 5 weeks ago by piyushjo • 100

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