User: mbio.kyle

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mbio.kyle330
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1 year, 8 months ago
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Posts by mbio.kyle

<prev • 54 results • page 1 of 6 • next >
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Help understanding Deseq2 '~group' contrasts
... Okay, so I have been using DESeq2 for a few months now and I think I have the hang of it. I am attempting a more complicated analysis and was hoping for some guidance / to be told what I am doing is 100% wrong. I have a fairly complicated set of samples which can be summarized as the following: I h ...
deseq2 de rna-seq written 3.1 years ago by mbio.kyle330 • updated 3.1 years ago by Devon Ryan90k
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Comment: C: Genome Browsers with BAM viewing capabilitites - Debian
... I will have a look at this. Thanks very much. ...
written 3.1 years ago by mbio.kyle330
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Comment: C: Genome Browsers with BAM viewing capabilitites - Debian
... Most of the java based applications tend to render very poorly. I have also just ran into alot of issues with getting things up and running (gathering dependencies, building, etc) ...
written 3.1 years ago by mbio.kyle330
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Answer: A: Genome Browsers with BAM viewing capabilitites - Debian
... So far http://goldenhelix.com/products/GenomeBrowse/ is winning. ...
written 3.1 years ago by mbio.kyle330
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Comment: C: Genome Browsers with BAM viewing capabilitites - Debian
... bigWig's are the usual endpoint for me, however I am specifically looking at differences in alignment calls between the two aligners. As such I need to look at the bam level, compare CIGAR strings, etc etc. ...
written 3.1 years ago by mbio.kyle330
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Genome Browsers with BAM viewing capabilitites - Debian
... Alright biostars, I am on my 4th genome browser (IGV, Savant, Bamview, samscope) and I just can't seem to find anything which works reasonably well. I am on Debian Jessie, running Awesome WM (this is probably part of my problem). I need to compare bam alignments between two different aligners (topha ...
bam visulization written 3.1 years ago by mbio.kyle330 • updated 3.1 years ago by Biostar ♦♦ 20
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Negative Zero Workaround in R for signed p-value sorting
... I am working with the results of a pathway analysis experiment. I have a dataframe, rows are pathways and and columns are samples. For each sample I did RNAseq, and performed GSEA on the results. I then pulled out each pathway from GSEA results (hallmark) from the positive and negative correlation a ...
R statistics written 3.2 years ago by mbio.kyle330 • updated 3.2 years ago by fanli.gcb660
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GSEA Prerank: Having Phenotype labels
... Hello, I am working with GSEAPrerank. I have generated my .rnk file and have successfully ran a preranked analysis. However there is no option for me to set phenotype labels or anything. So my reports end up with labels like "na-Pos" and "na-Neg". I'd like to be able to set those to some proper lab ...
prerank gsea rna-seq written 3.2 years ago by mbio.kyle330
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Comment: C: How to build a custom reference genome (from a BED file)
... RSEM works over top of a vanilla aligner (by default bowtie). It does tweak some parameters of the aligner, mostly with a focus on having bowtie return multiple alignments per read (which are fed into the EM model). The main reason for this is assigning reads to different isoforms. So it would not f ...
written 3.3 years ago by mbio.kyle330
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Answer: A: How to build a custom reference genome (from a BED file)
... You could look into using RSEM ([http://deweylab.biostat.wisc.edu/rsem][1]), it supports using a reference of just transcripts, and while it recommends using bowtie as its under the hood aligner, you can have it use STAR. You may need to do some data transformation on your bed file, or just get th ...
written 3.3 years ago by mbio.kyle330

Latest awards to mbio.kyle

Popular Question 2.1 years ago, created a question with more than 1,000 views. For UCSC BedGraph Issue
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Heatmap.2 R for differentially expressed genes DeSEQ2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Cuffdiff: 0 expression and NOTEST
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Tophat2 Reporting output tracks failed
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Tophat2 Reporting output tracks failed
Scholar 3.3 years ago, created an answer that has been accepted. For A: convert text file to VCF file ?

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