User: baldissera152

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Posts by baldissera152

<prev • 4 results • page 1 of 1 • next >
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TargetScan target genes are retired, should we use them?
... Hi, guys. I am using [TargetScan Fish][1], which has not been updated in a while, to find targets for a given miRNA. TargetScan Fish provides the gene IDs for representative 3'UTR target genes. I am using bioMart to find the names of these genes and find orthologous in other species. However, when ...
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Comment: C: DESeq2 design and Batch effects
... Thank you for your reply. You are right, it's very hard to analyze data when the design is very restrict. The groups I have defined as "acute" and "later" were based on the original paper's findings. My PCA just confirmed a grouping tendency. Regarding my idea of splitting a group based on the PCA ...
written 8 months ago by baldissera15210
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DESeq2 design and Batch effects
... Hi, guys. I am analyzing some RNA-Seq data from animals in different time points after a trauma in the spinal cord. The animal’s tissue have been pooled according to the time-points, therefore I do not have biological neither technical replicates. In order to analyze this data, I have attributed a ...
deseq2 design rna-seq batch effect written 8 months ago by baldissera15210 • updated 8 months ago by ATpoint36k
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Differential expression using Scran batch corrected data
... Hi, guys I intend to to integrate two single-cell RNA-Seq datasets and then correct their expression values for batch effect using Scran mnnCorrect function. However, after mnn correction, the output is a matrix which includes logtransformed and negative values. Since softwares usually require raw ...
single-cell batch correction scran rna-seq written 20 months ago by baldissera15210

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