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Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
SRA DESeq2
3.9 years ago Serge • 0
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Problem for Splitting reverse and forward reading in my RNA-seq
RNA-seq SRA reverse reads forward reads
6.8 years ago modarzi ▴ 10
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Uniting SRA Data into a single file
R fastq SRA sradb
updated 8.5 years ago by 25k • written 8.5 years ago by • 0
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download SRR*.lite.sra files using fastq-dump command
sra chipseqDB fastq-dump .lite.sra
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
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Search SRA based on BioSample Attributes
ncbi sra search
9.3 years ago massacomgrao • 0
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Tutorial: Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq biocparallel workflows sra Tutorial
9.8 years ago Sean Davis 21k
6 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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