User: Ron

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Ron480
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480
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Posts by Ron

<prev • 249 results • page 1 of 25 • next >
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Answer: A: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
... Here is another package that can be used : https://www.bioconductor.org/packages/devel/bioc/vignettes/DeconRNASeq/inst/doc/DeconRNASeq.pdf ...
written 10 days ago by Ron480
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Convert VCF to MAF from RNASeq mutation analysis
... Hi all, I am using this software for RNAseq mutation analysis: https://github.com/davidliwei/rnaseqmut My final output file is a VCF file and I want to convert it to a MAF file. I have come across these posts,however the output VCF from RNAseq is a bit different in this case. https://www.biostar ...
next-gen mutation rna-seq written 26 days ago by Ron480 • updated 24 days ago by Rafay Khan710
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Comment: C: Remove batch effect for differential expression
... Hi WouterDeCoster, I read this post,that I can use Combat batch normalization on Counts and then used the normalized values for differential expression with limma (not EdgeR and DESeq). What do you think on this? ...
written 4 weeks ago by Ron480
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Mouse Reads and Human Reads Similarity
... Hi all, This question is related to the post here: https://www.biostars.org/p/143019/ I am using BBMAP for separating human and mouse reads.Here is the output of statistics : #Matched 95918464 100.92671% #Name Reads ReadsPct Bases BasesPct hg19 79591774 83.74754 ...
next-gen bbmap rna-seq written 5 weeks ago by Ron480
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Comment: A: help with circos plot
... Check out Omic Circos . https://www.bioconductor.org/packages/devel/bioc/vignettes/OmicCircos/inst/doc/OmicCircos_vignette.pdf ...
written 5 weeks ago by Ron480
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Comment: C: Circos plot for ecoli genome
... You should probably look at the manual here where everything is explained: https://www.bioconductor.org/packages/devel/bioc/vignettes/OmicCircos/inst/doc/OmicCircos_vignette.pdf "In the following example, there are 10 segments, 10 individuals, 10 links, and 10 link polygons." Basically they are def ...
written 5 weeks ago by Ron480
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Comment: C: Circos plot for ecoli genome
... Your first circle should be made in the form of cytobands which form arcs of the circle.And then you can have mappings of genes (with positions)based on those cytobands. If you want to link those genes,there should be a separate data table for that. For each of arcs,mappings and links there should b ...
written 5 weeks ago by Ron480
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List of known fusions
... Hi all, Is there any list of known fusions database besides the COSMIC data base ? http://cancer.sanger.ac.uk/cosmic/fusion Thanks, Ron ...
fusion next-gen ngs rna-seq written 5 weeks ago by Ron480
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Answer: A: P-value calculation for gene expression data
... This code will work to get the p-values. Where you want to calculate p -values between Samples 1 to 5 as one category vs Samples 6 to 10 as another category.(dat here represents expression values) pv.list <- apply(dat,1, function(x) tryCatch( t.test(x[1:5],x[6:10],paired=TRUE)$p.value ...
written 6 weeks ago by Ron480
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Comment: C: samFilter Shows CoreDump
... Segmentation fault is usually because of less memory.You should provide more memory and re run. ...
written 6 weeks ago by Ron480

Latest awards to Ron

Popular Question 12 days ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 3 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Teacher 3 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
Popular Question 4 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Popular Question 6 months ago, created a question with more than 1,000 views. For Cufflinks output with filename prefix
Popular Question 6 months ago, created a question with more than 1,000 views. For Clustering of genes using FPKM
Popular Question 7 months ago, created a question with more than 1,000 views. For htseq-count for RNA Seq
Centurion 7 months ago, created 100 posts.
Popular Question 10 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 10 months ago, created a question with more than 1,000 views. For Extracting reads from multiple regions
Student 10 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 12 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 14 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 15 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ
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