User: gtho123

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gtho12340
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40
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New User
Location:
New Zealand
Last seen:
6 months, 1 week ago
Joined:
3 years ago
Email:
g******@aucklanduni.ac.nz

Posts by gtho123

<prev • 4 results • page 1 of 1 • next >
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DESeq2 time series contrasts between timepoints
... I have a RNA-Seq time series with two conditions (SD and LD) and 3 time points (0, 2, and 4). There are three biological replicates per sample. I have used DESeq2 to do a likelihood ratio test on the following designs:  full ~ condition + time + condition:time reduced ~ condition + time I underst ...
deseq2 rna-seq written 12 months ago by gtho12340 • updated 12 months ago by Michael Love19k
4
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bamsignals - bamcoverage has no strand-specific option??
... I am trying to create coverage plots from some strand specific BAM files and have run into the problem of the bamCoverage() function in the bamsignals package not having a strand specific option. This is not the case for the similar bamCount() and bamProfile() functions which only look at the 5` end ...
coverage bam bamsignals written 21 months ago by gtho12340 • updated 21 months ago by helmuth0
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makeTxDbPackage() ERROR: values for symbols SOURCEURL are not single strings
... I am trying to make a TxDb package from a gff3 file for an organism not available from UNSC. I can successfully make the TxDb like so: library(GenomicFeatures) txdb <- makeTxDbFromGFF(file="file.gff3", dataSource="Organism Genome Project", organi ...
genomicfeatures txdb written 23 months ago by gtho12340 • updated 23 months ago by James W. MacDonald48k
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Forge a BSgenome data package
... My supervisor has requested that I create coverage plots to visualize BAM alignments of RNA-Seq data. I though a good way to do this would be to use Gviz. We work on the model legume Medicago truncatula which does not have a BSgenome package so I though I'd try and make one. Following the vignette ...
bsgenome biostrings gviz written 3.1 years ago by gtho12340 • updated 3.1 years ago by Hervé Pagès ♦♦ 13k

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