User: LacquerHed

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LacquerHed0
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Posts by LacquerHed

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Multi-group DE scRNA-seq comps without replicates
... Wondering if its possible to do multi-group DE comparisons of 10X/Seurat data without replicates, using perhaps just the per-cell counts alone? To compare DE genes across clusters from lets say 2 genotypes and 2 treatments.Thanks. ...
scrna-seq deseq2 seurat rna-seq written 19 hours ago by LacquerHed0 • updated 13 hours ago by khorms140
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Comment: C: Seurat DESeq2 interaction terms
... If for instance I did not have replicates, how would you go about using the per-cell counts for more complex comparisons? Have the DESeq2 interaction part down, just wondering about other options. Thanks. ...
written 1 day ago by LacquerHed0
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Comment: C: Seurat DESeq2 interaction terms
... I do have biological replicates that allow pseudobulk-DE. Thanks for the suggestion. ...
written 2 days ago by LacquerHed0
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Seurat DESeq2 interaction terms
... Wondering if there is a good tutorial out the for differential expression analysis using interaction terms in Seurat with DESeq2? Like for instance if having two genotypes and two treatment conditions? Thanks! ...
deseq2 rna-seq seurat written 2 days ago by LacquerHed0
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Intersecting unbalanced BED files, normalizing for one
... Have two bed files I am intersecting, one of approximately 500 promoters +/- 2kb of TSS and the other some locations of histone marks within those promoters. There are many more intervals in the latter dataset, I would like to get the number of intersects that are unique to the promoter interval fil ...
bedtools bedops written 3 months ago by LacquerHed0

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