User: glady

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glady270
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Posts by glady

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Comment: C: Estrogen hormonal signalling genes
... And if I want to identify genes regulated in Males and Females, but also considering the differences between Tumor and Normal? Will a DESeq matrix with both conditions work for such an analysis? > dds = DESeqDataSetFromMatrix(data, colData, design = ~gender + > condition) [gender = male vs ...
written 15 hours ago by glady270
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Comment: C: Identifying cancer subtypes
... bulk tumor = RNA-seq data from the whole tumor. Not multiple datasets, I mean to say a single dataset (PDAC). is it possible to perform a separation of the tumor microenvironment in one dataset with some machine learning or clustering methods? ...
written 9 days ago by glady270
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Identifying cancer subtypes
... Hello, A bulk tumor data is made up of a complex microenvironment: stromal cells, fibroblasts, tumor cells, etc. Are there any machine learning or clustering methods that can perform a separation within a Tumor microenvironment, For example, if I pass on a dataset of the whole tumor from PDAC/lu ...
gene rna-seq written 9 days ago by glady270 • updated 4 days ago by Biostar ♦♦ 20
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comparative genomics BPGA
... Hello, I trying to perform a comparative genome analysis by BPGA, between two Streptomyces strains. The pipeline very correctly takes the two Protein FASTA files (downloaded from NCBI), as input. My query is that the core/accessory/uniques genes should get colored differently as we see in the ma ...
genome gene written 10 days ago by glady270
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Comment: C: antiSMASH error problem
... It worked with the accession number. Thanks ...
written 11 days ago by glady270
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Comment: C: Estrogen hormonal signalling genes
... Thank you for your reply. By functional enrichment analysis, you mean performing a GO study or GSEA? ...
written 11 days ago by glady270
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antiSMASH error problem
... I'm trying to predict secondary metabolites in a Streptomyces genome downloaded from NCBI. But when I pass the GeneBank file on the antiSMASH query submission page, I get error: failed: Job returned errors: ERROR 23/02 17:59:21 all records skipped What's wrong? What parameter should I ...
genome gene written 11 days ago by glady270 • updated 11 days ago by Ram32k
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Estrogen hormonal signalling genes
... Hello, I have downloaded gene expression data for NSCLC Tumor tissues from TCGA, it contains both Tumor_male and tumor_females. How can I identify genes that are specifically regulated in NSCLC by estrogen hormonal signalling? 1) Will DESeq2 between the tumor_male and tumor_female give me the re ...
rna-seq written 11 days ago by glady270
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Comment: C: Over-expression of genes
... Thank you for your reply, sir. I have some PDAC samples, how can I say a certain number of genes are over-expressed in this condition? I understand that Up/downregulation of a gene is a natural process, while over-expression is induced artificially but does these two terms Up-regulation and over-ex ...
written 28 days ago by glady270
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Over-expression of genes
... What causes over-expression of a gene? And what is the difference between over expression and up-regulation? Is there a way to measure expression profiles of genes, if they are over expressed? ...
genome gene rna-seq written 29 days ago by glady270 • updated 28 days ago by seidel7.4k

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