User: Ron

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Ron970
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970
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5 years, 9 months ago
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Posts by Ron

<prev • 318 results • page 1 of 32 • next >
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Visualize gene fusions in IGV
... Hi, I am trying to visualize gene fusions from RNAseq data in IGV, that is detected by gene fusion software STAR-fusion and Fusion catcher. Does anybody know of steps to do this? I always find it complex to how to color,sort, group the reads so as to visualize the gene fusion. This post is informa ...
next-gen rna-seq written 4 months ago by Ron970
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Comment: C: Tool to separate human and mouse rna seq reads
... STAR + featurecount/htseq-count is a very good pipeline to use. ...
written 5 months ago by Ron970
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Answer: A: Gene expression profile analysis
... Also EBseq. http://bioconductor.org/packages/release/bioc/html/EBSeq.html It provides different possible patterns between multiple conditions. ...
written 5 months ago by Ron970
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Comment: C: Drugs targeting Gene Fusions
... So it is best to look at drug interactions with the gene fusion themselves ? I mean , A drug that would work for lets say ERBB2--CDK12 fusion would not work for ERBB2--PGAP3 fusion ? Or it can be considered druggable , based on how the gene fusion product is ? On the contrary, it seems NTRK fusion ...
written 6 months ago by Ron970
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Drugs targeting Gene Fusions
... Hello , I wanted to know if gene fusions from RNAseq data can be said druggable based on one of the genes being druggable or it has to be druggable as a fusion ? I would like to look into the drugs that bind to the genes from fusions,so which one would be the right way to look into the data. This ...
next-gen rna-seq written 6 months ago by Ron970 • updated 6 months ago by zepper40
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Comment: C: Drug to Target/Gene/Protein Interaction Databases
... hello @Malachi Does this database (http://dgidb.org/downloads ) includes information from the resources listed above? or could you provide info on how it was created ? I read this page and http://dgidb.org/getting_started "drug-gene interactions have been mined from DrugBank, therapeutic target da ...
written 6 months ago by Ron970
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Comment: C: Plots in R for bioinformatics analyses
... I posted the link to the data and the paper. ...
written 6 months ago by Ron970
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How to recreate this dot plot?
... Hi all, Does somebody know which package can be used for plots like this? > The dot plots illustrates the number of detected fusion transcripts per megabase per sample normalized by the sequencing coverage. Tumor types were sorted according to the fraction of samples with fusions. I am tryi ...
R next-gen rna-seq written 6 months ago by Ron970 • updated 6 months ago by zx87548.3k
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Answer: A: Saving individual clusters from heatmaps
... For extracting the clusters based on Columns.(ComplexHeatmaps) mat = matrix(rnorm(80, 2), 8, 10) mat = rbind(mat, matrix(rnorm(40,-2), 4, 10)) rownames(mat) = letters[1:12] colnames(mat) = letters[1:10] HM <- Heatmap(mat, km=3 , column_km = 3) HM for (i in 1:len ...
written 7 months ago by Ron970
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Comment: C: Counting number of base pairs and features in each bed file
... A follow up question - I also want to count the percentage of UTR's ,exons in my bed file ,so the way would be downloading a bed file for both of them separately(UTR's ,exons) and doing the intersect with the complete bed file of interest? ...
written 8 months ago by Ron970

Latest awards to Ron

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Assigning scoring metric to a cluster
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Plotting RPKMS per chromosome
Popular Question 3 months ago, created a question with more than 1,000 views. For Plotting RPKMS per chromosome
Popular Question 3 months ago, created a question with more than 1,000 views. For Assigning scoring metric to a cluster
Student 5 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Great Question 5 months ago, created a question with more than 5,000 views. For GSEA Preranked analysis on RNA-SEQ
Appreciated 5 months ago, created a post with more than 5 votes. For Interpreting GSEA results
Popular Question 5 months ago, created a question with more than 1,000 views. For Working with human database in Kraken
Popular Question 5 months ago, created a question with more than 1,000 views. For Working with human database in Kraken
Popular Question 6 months ago, created a question with more than 1,000 views. For Working with human database in Kraken
Great Question 7 months ago, created a question with more than 5,000 views. For GSEA Preranked analysis on RNA-SEQ
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: pca analysis for differential gene expression data of microarray samples of simi
Scholar 7 months ago, created an answer that has been accepted. For A: How to import huge .csv files in R studio?
Great Question 7 months ago, created a question with more than 5,000 views. For GSEA Preranked analysis on RNA-SEQ
Epic Question 7 months ago, created a question with more than 10,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 10 months ago, created a question with more than 1,000 views. For Validating Predictions Of Small Insertions / Deletions
Popular Question 11 months ago, created a question with more than 1,000 views. For Validating Predictions Of Small Insertions / Deletions
Great Question 12 months ago, created a question with more than 5,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 12 months ago, created a question with more than 1,000 views. For Working with human database in Kraken
Popular Question 12 months ago, created a question with more than 1,000 views. For Validating Predictions Of Small Insertions / Deletions
Student 12 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 13 months ago, created a question with more than 1,000 views. For Validating Predictions Of Small Insertions / Deletions
Popular Question 14 months ago, created a question with more than 1,000 views. For Validating Predictions Of Small Insertions / Deletions
Popular Question 15 months ago, created a question with more than 1,000 views. For Validating Predictions Of Small Insertions / Deletions
Student 15 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ

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