User: Zhilong Jia

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Zhilong Jia1.5k
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a bioinformatician

Posts by Zhilong Jia

<prev • 245 results • page 1 of 25 • next >
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Tools to infer population structure and evolution from structural variation genotype data
... Are there tools to infer population structure and evolution from structural variation genotype data? Generally, [fastStructure][1] or other tools are designed for SNPs. Are inferring population structure and evolution from structural variation genotype data largely different from that from SNP gen ...
population structure structural variation written 4 months ago by Zhilong Jia1.5k • updated 9 weeks ago by Biostar ♦♦ 20
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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 17 months ago by Zhilong Jia1.5k
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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 17 months ago by Zhilong Jia1.5k
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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 17 months ago by Zhilong Jia1.5k
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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 18 months ago by Zhilong Jia1.5k
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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 18 months ago by Zhilong Jia1.5k
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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 18 months ago by Zhilong Jia1.5k
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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 18 months ago by Zhilong Jia1.5k
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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 18 months ago by Zhilong Jia1.5k
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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 18 months ago by Zhilong Jia1.5k

Latest awards to Zhilong Jia

Popular Question 26 days ago, created a question with more than 1,000 views. For what does lowess smoothed line show in a MA plot
Scholar 4 weeks ago, created an answer that has been accepted. For A: Batch effect removal before merging microarray data sets
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Popular Question 3 months ago, created a question with more than 1,000 views. For what does lowess smoothed line show in a MA plot
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How can we make this plot? (sequence logo)
Popular Question 8 months ago, created a question with more than 1,000 views. For what does lowess smoothed line show in a MA plot
Popular Question 8 months ago, created a question with more than 1,000 views. For what does lowess smoothed line show in a MA plot
Popular Question 10 months ago, created a question with more than 1,000 views. For what does lowess smoothed line show in a MA plot
Popular Question 14 months ago, created a question with more than 1,000 views. For what does lowess smoothed line show in a MA plot
Popular Question 16 months ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Great Question 17 months ago, created a question with more than 5,000 views. For how to set the size of cell of heatmap.2 in R
Popular Question 18 months ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Popular Question 18 months ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Popular Question 19 months ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Great Question 21 months ago, created a question with more than 5,000 views. For how to set the size of cell of heatmap.2 in R
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: How can we make this plot? (sequence logo)
Popular Question 21 months ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Popular Question 22 months ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Popular Question 23 months ago, created a question with more than 1,000 views. For which structure should be used for a drug (like fluvastatin) in chemoinformatics
Student 2.0 years ago, asked a question with at least 3 up-votes. For Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How can we make this plot? (sequence logo)
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to calculate connectivity score for a compound in connectivity map O2?
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Popular Question 2.2 years ago, created a question with more than 1,000 views. For A list of Bioinformatics projects for volunteers

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