User: tunl

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tunl40
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Posts by tunl

<prev • 62 results • page 2 of 7 • next >
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Question about downloading RNA-seq long reads and short reads for the same sample
... We need to use RNA-seq long reads and short reads from the same sample to do some comparisons. I was wondering which websites may have both RNA-seq long reads (e.g. PacBio reads) and short reads for the same sample so we could download from there? Any advice would be greatly appreciated. Thank you ...
long reads rna-seq pacbio written 7 days ago by tunl40 • updated 6 days ago by magdoll10
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Comment: C: Question about some features in Cytoscape.js (or D3.js)
... Thanks a lot! So Cytoscape.js is easier to program with than D3.js right? If I go with Cytoscape.js by sacrificing some features, how hard would it be for me to pick up Javascript and work with Cytoscape.js? Thanks again! ...
written 7 months ago by tunl40
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Comment: C: Question about some features in Cytoscape.js (or D3.js)
... Thank you so much for your advice! Actually, what I mean about “we need to show the network in layers” is that we have 3 different types of nodes, we want to put each type of nodes at different locations (bottom, middle, and top) of the window, but there are edges between different types of nodes. ...
written 7 months ago by tunl40
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Comment: C: Question about some features in Cytoscape.js (or D3.js)
... Thank you a lot for your advice! I’m a java programmer, but I never used javascript before. Could you please give me some ideas about how hard (and how long) it would be to pick up javascript for someone who can program in java? So if Cytoscape.js can support these features, does it mean Cytoscape ...
written 7 months ago by tunl40
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Comment: C: Question about some features in Cytoscape.js (or D3.js)
... Thank you so much for your advice! We'd need to put this on a website. And the number of nodes could be a lot and is up to the user's input. We will set these features by default through programming, but users can change other settings manually if they want. So I guess we'd need it to be interacti ...
written 7 months ago by tunl40
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Question about some features in Cytoscape.js (or D3.js)
... We need to use a network visualization tool to display our protein interaction network. We need to automatically represent different types of nodes in different shapes and colors, represent different node prizes in varying darkness of node, and represent different edge weights in varying width of e ...
d3.js network visualization cytoscape.js written 7 months ago by tunl40 • updated 7 months ago by Alex Reynolds20k
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Comment: C: What exactly one "library" corresponds to in RNA-seq analysis
... Thanks a lot! On the metadata table I received, for each sample there are two tubes. Does this mean there are two technical replicates for each sample? If so, there would be 2 libraries for each sample, right? Also, for each tube, there are 3 lanes. Does number of lanes have anything to do with n ...
written 7 months ago by tunl40
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Comment: C: What exactly one "library" corresponds to in RNA-seq analysis
... Thank you so much! So you mean, each biological replicate leads to one library, right? So in our case (two conditions and each condition has 4 replicates), we have totally 8 libraries. ...
written 7 months ago by tunl40
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Comment: C: What tools are better than Cuffdiff for differential expression analysis
... Thank you for your advice! So you think DESeq2 and edgeR are more accurate than Cuffdiff? They are faster than Cuffdiff. But Cole Trapnell (Cuffdiff author) believes DESeq and edgeR (the tools that test raw gene-level counts) are less accurate than Cuffdiff, since they assume that isoforms have ...
written 7 months ago by tunl40
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What tools are better than Cuffdiff for differential expression analysis
... I heard that Cuffdiff is no longer considered as a very good tool for differential expression analysis. I am wondering what the major issues are in Cuffdiff ? What tools are better than Cuffdiff for differential expression analysis? Thank you very much for your advice! ...
cuffdiff rna-seq differential expression analysis written 7 months ago by tunl40

Latest awards to tunl

Popular Question 6 months ago, created a question with more than 1,000 views. For Coverage-search vs. no coverage-search in running Tophat
Supporter 13 months ago, voted at least 25 times.

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