User: Zhilong Jia

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Zhilong Jia1.4k
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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 Jia1.4k
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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 Jia1.4k
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Comment: C: edger model matrix design of linear model
... 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 Jia1.4k
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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 Jia1.4k
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Answer: A: A good pipeline for GO term analysis on RNA-seq Clusters in R?
... 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 Jia1.4k
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Comment: C: KeggExp: a web server for visualizing KEGG pathways maps when analyzing expressi
... 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 Jia1.4k
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Comment: A: BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, v
... An enhancement : a function to transform the input matrix. ...
written 3 months ago by Zhilong Jia1.4k
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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 Jia1.4k
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Comment: C: KeggExp: a web server for visualizing KEGG pathways maps when analyzing expressi
... 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 Jia1.4k
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Comment: C: How to add images to a Biostars post
... 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 Jia1.4k

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