User: gtho123

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gtho12340
Reputation:
40
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New User
Location:
New Zealand
Last seen:
1 year, 7 months ago
Joined:
4 years, 2 months ago
Email:
g******@aucklanduni.ac.nz

Posts by gtho123

<prev • 4 results • page 1 of 1 • next >
3
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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 2.1 years ago by gtho12340 • updated 2.1 years ago by Michael Love26k
4
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1
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714
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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 2.8 years ago by gtho12340 • updated 2.8 years ago by helmuth0
2
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505
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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 3.0 years ago by gtho12340 • updated 3.0 years ago by James W. MacDonald52k
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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 4.2 years ago by gtho12340 • updated 4.1 years ago by Hervé Pagès ♦♦ 14k

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Popular Question 19 months ago, created a question with more than 1,000 views. For DESeq2 time series contrasts between timepoints

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