User: Zhilong Jia
Zhilong Jia • 1.4k
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a bioinformatician
Posts by Zhilong Jia
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Comment:
C: Downloading Data From Mg-Rast
... http://api.metagenomics.anl.gov/metadata/export/mgp128
ref: http://api-ui.mg-rast.org/api.html#sample ...
written 9 weeks ago by
Zhilong Jia • 1.4k
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Comment:
C: Downloading Data From Mg-Rast
... File 050.2 - This is the unfiltered metagenome that was originally uploaded to MG-RAST
File 100.1 - preprocess.passed.fna
File 100.2 - preprocess.removed (low quality)
File 350.2 & 350.3 - These are the protein coding genes (amino acids and nucleotides)
File 440.1 - These are ...
written 9 weeks ago by
Zhilong Jia • 1.4k
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... in line 4, it should be: ` foo <- data.frame(SampleType = paste0(rep(c("A","B"), each = 3)), Reps = rep(1:3, 2),` `Names = paste0(rep(c("A","B"), each=3), rep(1:3, 2) ) )`
`set.seed()` before generating the data will be helpful.
...
written 3 months ago by
Zhilong Jia • 1.4k
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431
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Answer:
A: RNA-seq cluster analysis in R
... 0. [clusterProfiler][1]. [Visualization of profile comparison][2] section from Bioconductor package `clusterProfiler`. A quick solution for your question.
see ![figure][3].
1. [co-expressed gene set enrichment analysis, cogena][4]. `cogena` started with gene expression not clustered genes, While i ...
written 3 months ago by
Zhilong Jia • 1.4k
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397
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... 0. [the toppcluster webserver][1], but not work recently.
1. [co-expressed gene set enrichment analysis, cogena][2]. But Zebrafish GO gene sets as a gmt file are needed.
2. clusterProfiler. `GO analyses (groupGO(), enrichGO() and gseGO()) support organisms that have an OrgDb object available.` so it ...
written 3 months ago by
Zhilong Jia • 1.4k
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... 1. try to download it at the deployed website. you will see the downloaded files as follow.
![enter image description here][1]
2. `The expression profile data should be processed data, in which the fold change of one gene between group A and group B could be calculated with ValueA/ValueB`. Actually ...
written 3 months ago by
Zhilong Jia • 1.4k
2
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1
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877
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1
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... An enhancement : a function to transform the input matrix. ...
written 3 months ago by
Zhilong Jia • 1.4k
0
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161
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Answer:
A: Heatmap2 code error
... Add `Colv=NA` to `heatmap.2(as.matrix(X), col=redgreen(75), scale="row", key=T, keysize=1.5, ` `density.info="none", trace="none",cexCol=0.9, labRow=NA, Colv=NA)`.
For detail, see manual of `gplots::heatmap.2`
BTW, see https://www.biostars.org/p/309884/ to get how to upload figures. `https://i.i ...
written 3 months ago by
Zhilong Jia • 1.4k
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... Powerful. I will recommend to my colleagues. Two small bugs. 1. the try samples cannot be downloaded correctly. 2.heatmap cannot show negative value. BTW, how does it calculate the group expression per gene?
For 1. ![enter image description here][1]
For 2. ![enter image description here][2]
[1 ...
written 3 months ago by
Zhilong Jia • 1.4k
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... I'm not familiar with python. It's a shame. However, I filed an issue at [github][1] and gave a simple solution that more tips during the poped inserting figure page. Thank you.
[1]: https://github.com/ialbert/biostar-central/issues/455 ...
written 3 months ago by
Zhilong Jia • 1.4k
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