User: wangdp123

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wangdp12390
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Posts by wangdp123

<prev • 28 results • page 1 of 3 • next >
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Tool: GCevobase: an evolution-based database for GC content in eukaryotic genomes
... Hi there, I am happy to introduce a new database that contains the essential genome composition information from 1118 eukaryotic genomes that includes GC content, GC1, GC2, GC3 and GC4d (GC content at four-fold degenerate sites). The relevant reference: GCevobase: an evolution-based database for ...
genome gc content evolution tool written 18 days ago by wangdp12390
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How to find the hub genes in the gene co-expression network constructed by WGCNA
... Hi there, I have used WGCNA tool to construct a gene co-expression network and identified several modules. I am keen to discover the hub genes (the gene that has the maximum connections with other genes in a module) in each module. Does anybody know how to pinpoint the hub genes? Via which scripts ...
wgcna hub gene written 4 weeks ago by wangdp12390 • updated 4 weeks ago by Kevin Blighe13k
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Comment: C: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc
... Hi Kevin, Your detailed answer is highly appreciated. I have a further question. In fact, I have about 40000 genes with FPKMs for the network construction, and I try to increase maxBlockSize = 40000, in which way the calculation is running extremely slow. In this case, do you think I need to fil ...
written 3 months ago by wangdp12390
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The RNA-Seq data input for WGCNA in terms of gene co-expression network construction
... Hi there, I am learning to use RNA-Seq data matrix with WGCNA to build up gene-co-expression network. I know WGCNA was designed for the microarray data but after appropriate handling, it is also applicable to the RNA-Seq data. Regarding the format of the input data, I have several concerns: 1. T ...
wgcna network written 3 months ago by wangdp12390 • updated 3 months ago by Kevin Blighe13k
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The strategy to annotate the transcriptional factors from transcripts
... Hi there, I have found that the plantdb database is quite useful in my work. I have tried two different ways to annotate the transcription factors for my transcripts. 1. Blastx my transcript sequences against protein sequences of All TFs in PlantTFDB 4.0. 2. Use the functional module of Transcrip ...
annotation tf written 5 months ago by wangdp12390
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Comment: C: Draw the phylogeny from RNA-Seq data
... Hi, thanks for this. I have looked through the log2, rlog and VST normalization methods mentioned in this workflow. But my data are from different species, so in this case, I believe that some calculations should be made to normalize the gene lengths. Any thought about this? ...
written 7 months ago by wangdp12390
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Draw the phylogeny from RNA-Seq data
... Hi there, I am trying to use RNA-Seq data from a large number of samples to draw the phylogenetic tree based on FPKM values in order to show the relationship among all samples. (The samples include various species, tissues and treatments.) Are there any elegant tools implemented for this purpose? ...
phylogeny species tissues treatment rna-seq written 7 months ago by wangdp12390 • updated 6 months ago by Biostar ♦♦ 20
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How to understand "between_species_paralog" in Ensembl and EnsemblGenomes
... Hi there, I am trying to understand how to define "between_species_paralog" in Ensembl and EnsemblGenomes and found out the definitions here: For Ensembl: (http://www.ensembl.org/info/genome/compara/homology_method.html) > Currently, we only annotate between_species_paralog when there is no &g ...
ensembl ensemblgenomes paralogs written 7 months ago by wangdp12390 • updated 7 months ago by Emily_Ensembl14k
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How to rank genes prepared for GSEA analysis with TopGO
... Hi there, I am trying to use TopGO to perform some GSEA analyses (Gene Set Enrichment Analysis). In order to do this, I have done the differential expression analysis for all genes and produced the P-values and Fold change values for each gene. I am aware of the fact that TopGO needs a ranked gene ...
topgo gsea rna-seq written 8 months ago by wangdp12390 • updated 8 months ago by kennethcondon20071.1k
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How to obtain more GO terms for transcripts
... Hi there, I am working on the annotation of genes assembled from RNA-Seq data from a non-model species and I have tried to use interproscan to get the GO terms based on the protein sequences predicted by Transdecoder. It seems that only a limited number of genes have predicted ORF and only a propor ...
de novo assembly gene ontology written 8 months ago by wangdp12390 • updated 8 months ago by Whoknows630

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