User: Mehmet

gravatar for Mehmet
Mehmet230
Reputation:
230
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Trusted
Location:
Japan
Last seen:
21 hours ago
Joined:
3 years ago
Email:
m*********@duzce.edu.tr

Posts by Mehmet

<prev • 251 results • page 1 of 26 • next >
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Genome wide transcription binding site in a worm species
... Dear All, I searched in the internet and I could not find a proper way to follow steps to find transcription binding sites using genome and/or RNA-seq data. I have genome and RNA-seq data (also Differentially expressed gene list) of a worm species, and I want to find transcription binding sites of ...
genome rna-seq sequencing written 6 days ago by Mehmet230
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Comment: C: Gene set enrichment analyses of different samples of the same species
... Thank you for reply. 1. Instead of conditions, I have life stages starting from egg to adults (total 8 stages). 2.I have a peptidase gene set that has 5 subfamilies like aspartic, metallo, ... A total of 800 genes are peptidase and belong to 5 subfamilies. These genes have FPKM values. I want to kn ...
written 9 days ago by Mehmet230
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Gene set enrichment analyses of different samples of the same species
... Dear All, I want to perform gene set enrichment analysis of a species using specific gene families. I have a peptidase gene list that have different peptidase families (Aspartic, metal, serine etc.), and these genes have FPKM values at different life stage of the same organisms. Some genes have ze ...
genome gene rna-seq written 9 days ago by Mehmet230 • updated 8 days ago by Brian Gudenas90
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Comment: C: RepeatModeler No families identified
... Hi When I used these; A) make a database /bin/RepeatModeler/BuildDatabase -name mydatabase my.genome.fa B) Run database /bin/RepeatModeler/RepeatModeler -database mydatabase #output of RepeatModeler: consensi.fa.classified ...
written 23 days ago by Mehmet230
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Comment: C: Metagenomic analysis workflow
... Can you clarify these: What are your organisms? Fungus, bacteria? What do you want to do via metagenomics? species diversity or identification in your samples? ...
written 4 weeks ago by Mehmet230
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Comment: C: How to find category names of Gene Ontoloy based on category ID
... Hi Leite, Thanks. but I have a lot of GO Ids, so I need a way to put all Ids and get results.Do you have any idea for this? ...
written 6 weeks ago by Mehmet230
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How to find category names of Gene Ontoloy based on category ID
... Dear All, I have a data set that has category IDs as below: Category 1 GO:0016021 2 GO:0044425 3 GO:0031224 4 GO:0004872 I want to find what category they belong to (Molecular function, cellular component and biological process) Any idea about that? ...
gene rna-seq written 6 weeks ago by Mehmet230 • updated 6 weeks ago by Pierre Lindenbaum103k
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Comment: C: How to order columns of heatmap as they are in matrix data
... Hi Kevin, Now it is okay, I figured it out. Here is my command: hmap <- Heatmap(heat, name="Z-score",col=colorRamp2(myBreaks, myCol), cluster_columns = FALSE, heatmap_legend_param=list(color_bar="continuous", legend_direction="horizontal", legend_width=unit(3,"cm"), title_position="topcen ...
written 7 weeks ago by Mehmet230
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Comment: C: How to order columns of heatmap as they are in matrix data
... I don't know how to paste data as it is readable. Please follow the previous topic (Heatmap based with FPKM values). ...
written 7 weeks ago by Mehmet230
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How to order columns of heatmap as they are in matrix data
... Dear All, I made a complex heatmap using complexheatmap package of R. I want to order columns of the heatmap based on order in my matrix data. Any idea? this is heatmap command I run: hmap <- Heatmap(heat, name="Z-score",col=colorRamp2(myBreaks, myCol), column_order = samplesnames, clust ...
R rna-seq written 7 weeks ago by Mehmet230

Latest awards to Mehmet

Supporter 9 weeks ago, voted at least 25 times.
Popular Question 4 months ago, created a question with more than 1,000 views. For phylogenetic tree after ortholog finding by orthoMCL
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