User: Kurban

gravatar for Kurban
Kurban170
Reputation:
170
Status:
Trusted
Location:
china/Urumqi/xinjiang academy of animal scinces
Last seen:
10 months, 3 weeks ago
Joined:
5 years, 3 months ago
Email:
k********@sina.com

New born child to bio informatics with the biology background.

Posts by Kurban

<prev • 104 results • page 1 of 11 • next >
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There any tools for gene regulation network visualizing?
... Hello guys, I have a set of transcription factors and their target genes (TF-TG connection), and their expression data from RNA-seq at a certain treatment and control conditions. Here, I want to visualize this network, including hub and connection edges. Could you recommend some tools to do that? If ...
tf-tg connection regulatory network written 20 months ago by Kurban170
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Comment: C: How to cluster differential expressed genes from RNA-seq analysis?
... hi @ WouterDeCoster, i know that count data is in integers, but i want to use RPKM/FPKM value for heatmap ...
written 2.6 years ago by Kurban170
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Comment: C: How to cluster differential expressed genes from RNA-seq analysis?
... hi @ b.nota, i checked the heatmap.2 in gplots package and got the heatmap of my data based on FPKM values. but the number of my input genes are more than a thousand,and i want to extract the clustering result of the heatmap, how can i do that? ...
written 2.6 years ago by Kurban170
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Comment: C: How to cluster differential expressed genes from RNA-seq analysis?
... thank you @ e.rempel, DESeq2 dose cluster DEGs based on the count data, but it only accept integer value. ...
written 2.6 years ago by Kurban170
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Comment: C: How can I get DESeq2 heatmap result in tabular format?
... hi @e.rempel, could not cut the tree, and reported this error: > cutree(cluster.object$tree_col,60) Error in cutree(cluster.object$tree_col, 60) : invalid 'tree' ('merge' component) ...
written 2.6 years ago by Kurban170
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How can I get DESeq2 heatmap result in tabular format?
... Hello guy, I have use DEseq2 got the heat map based on unigenes’ readcounts. The command lines I have used are: colData <- read.table("colData.txt") countData <- read.table("countData_DEGs(count_larger_1).txt") rownames(colData) <- sub("fb","",rownames(colData)) all(rownames(colData) %in ...
rna-seq written 2.6 years ago by Kurban170 • updated 2.6 years ago by e.rempel780
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How to cluster differential expressed genes from RNA-seq analysis?
... Hello guys, I have transcriptome data from low temperature treated samples with different time length. And I got different number of DEGs for each time point of strass challenge. Now I want to cluster all these differentially expressed genes. In some papers they did this analysis by heatmap based o ...
rna-seq written 2.7 years ago by Kurban170
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About TF-TG files
... I have downloaded the data of TF2DNA database. Following is the Drosophila pscan file : ---------- tf_name target_name start_position end_position direction binding_score p_value binding_sites ---------- ab alph 25417302 25417602 (+) 1474.07 0.000006 25417355:1474.07:0.000006 ---------- ab ...
alignment written 2.9 years ago by Kurban170
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Answer: A: Removing redundant sequences
... Hello guys. I have more than 70,000 protein sequences come from 65 animal species, most of them are TFs. So some of them might be homologous. I like to use CD-HIT to remove the them. But which similarity threshold should I use? Any suggestion? ...
written 3.0 years ago by Kurban170
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is there any source for TF(transcription factor)-TG(target gene)?
... Hello guys, I have more than 800 animal transcription factor sequences from ensemble. I want to find their target gene sequences. Could anyone tell how could I do that? Is there any source (or database) for TF(transcription factor)-TG(target gene) information of Drosophila Melanogaster and Caenorha ...
sequence written 3.0 years ago by Kurban170 • updated 3.0 years ago by Macspider3.0k

Latest awards to Kurban

Popular Question 19 months ago, created a question with more than 1,000 views. For about Blastx generated file
Popular Question 19 months ago, created a question with more than 1,000 views. For multiple nucleotide sequences align to multiple protein sequences
Popular Question 19 months ago, created a question with more than 1,000 views. For transcription factor database
Popular Question 19 months ago, created a question with more than 1,000 views. For about annotate transcriptome
Popular Question 19 months ago, created a question with more than 1,000 views. For Predicte Protein-Protein Interactions
Popular Question 19 months ago, created a question with more than 1,000 views. For Are there tools for finding ORF for multiple sequences
Popular Question 21 months ago, created a question with more than 1,000 views. For about Blastx generated file
Popular Question 2.5 years ago, created a question with more than 1,000 views. For about Blastx generated file
Popular Question 2.5 years ago, created a question with more than 1,000 views. For multiple nucleotide sequences align to multiple protein sequences
Popular Question 2.5 years ago, created a question with more than 1,000 views. For about annotate transcriptome
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Predicte Protein-Protein Interactions
Centurion 2.6 years ago, created 100 posts.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For multiple nucleotide sequences align to multiple protein sequences

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