scFlow
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combiz
Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
Hi @Al-Murphy, I am re-running the scFlow.Rmd, however report_qc_sce function throws the error below, cannot read overview.Rmd from system.files. ```{r eval=TRUE} #Store results in same temp dir report_qc_sce(sce, report_file =...
**Describe the bug** I am getting an error trying to download the scFlow package using devtools. **To Reproduce** I run the following code in R and get this error: ```...
The 'neurogenomics/EWCE' package should be updated to use the latest version at `NathanSkene/EWCE'. This will require a refactoring of the code due to major updates to EWCE.
For QC of single-nucleus RNA-sequencing, only need to look for outliers in the higher tail of mitochondrial counts, as good quality nuclei should not contain any mitochondrial transcripts. Thus, added...
## Description of feature request When thresholding mitochondrial content, `scater::isOutlier()` is used with the argument `type = "both"`. This tests both tails of the distribution of mitochondrial content for outliers....
The LIANA framework simplifies cell-cell interaction analyses with multiple tools: https://github.com/saezlab/liana
Updates include: - added Sankey plot (riverplot) feature to the integrate report (#144) - added proportional barplot feature to the integrate report showing what percentage of each cluster comes from...
**Describe the bug** Error while running the `perform_de()` function **To Reproduce** Steps to reproduce the behavior: 1. In R: ``` # Performing differential expression analysis following by impacted pathway analysis...
**Describe the bug** Unable to run the steps in the Vigenette. Section Step four – Merging multiple datasets into one SingleCellExperiment object **To Reproduce** Steps to reproduce the behavior: 1....
