User: wangdp123

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wangdp12360
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Posts by wangdp123

<prev • 23 results • page 1 of 3 • next >
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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 8 weeks 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 8 weeks ago by wangdp12360 • updated 5 weeks 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 9 weeks ago by wangdp12360 • updated 9 weeks 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 11 weeks ago by wangdp12360 • updated 11 weeks ago by kennethcondon2007810
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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 3 months ago by wangdp12360 • updated 3 months ago by Whoknows590
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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 3 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 3 months ago by wangdp12360 • updated 3 months ago by mforde84830
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Comment: C: Generate syntenic blocks between two vertebrates
... Hi, here is another option for genome alignment in a unit of genes. Good to try: http://ec2-52-40-200-174.us-west-2.compute.amazonaws.com/LCGserver/ ...
written 4 months ago by wangdp12360
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Comment: C: Bulky collection of the orthologs and paralogs data from Ensembl
... Hi, Thank you for the explanation. Any clue to understand the tables in Compara.88.protein_default.nh.emf.gz and Compara.88.protein_default.nhx.emf.gz and parse them if I try to identify the one-to-one, one-to-many and many-to-many relations? Cheers, Tom ...
written 4 months ago by wangdp12360
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Bulky collection of the orthologs and paralogs data from Ensembl
... Hi there, I am trying to retrieve all the orthologs and paralogs for all fungi species in ensembl fungi database, but I couldn't find a way to download them in bulk. I know Biomart provides the service for manual collection but it doesn't work for my purpose. For example, I would like to download ...
orthologs ensembl paralogs written 4 months ago by wangdp12360

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