User: wangdp123

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wangdp12360
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Posts by wangdp123

<prev • 26 results • page 1 of 3 • next >
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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 23 days ago by wangdp12360
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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 24 days ago by wangdp12360 • updated 23 days ago by Kevin Blighe7.2k
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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 9 weeks ago by wangdp12360
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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 4 months ago by wangdp12360
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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 4 months ago by wangdp12360 • updated 3 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 4 months ago by wangdp12360 • updated 4 months ago by Emily_Ensembl13k
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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 4 months ago by wangdp12360 • updated 4 months ago by kennethcondon2007930
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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 5 months ago by wangdp12360 • updated 5 months ago by Whoknows600
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Comment: C: Software for GO enrichment based on own DEGs and GO annotation.
... Hi, it is not a model organism. I have annotated the GO terms for each gene in this species. What I need to do is to input my GO assignment rather than use the public annotated one to do enrichment analysis with my identified up-regulated or down-regulated gene lists. ...
written 5 months ago by wangdp12360
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Software for GO enrichment based on own DEGs and GO annotation.
... Hi there, I have assigned all GO terms to each gene in my study through interproscan, and I am going to do some GO enrichment analysis based on my DEGs and my GO annotation database. Could anybody suggest some decent software for this purpose? Many thanks, Tom ...
enrichment go written 5 months ago by wangdp12360 • updated 5 months ago by mforde841000

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