Single-cell/nuclei pipeline for data derived from Oxford Nanopore
polya_liftover - sc/snRNAseq Snakemake Workflow
A [Snakemake][sm] workflow for using PolyA_DB and UCSC Liftover with Cellranger.
Some genes are not accurately annotated in the reference genome. Here, we use information provide by the [PolyA_DB v3.2][polya] to update the coordinates, then the [USCS Liftover][liftover] tool to update to a more recent genome. Next, we use [Cellranger][cr] to create the reference and count matrix. Finally, by taking advantage of the integrated [Conda][conda] and ...
scRNA-Seq pipelines
Here we forge the tools to analyze single cell RNA-Seq experiments. The analysis workflow is based on the Bioconductor packages scater and scran as well as the Bioconductor workflows by Lun ATL, McCarthy DJ, & Marioni JC [*A step-by-step workflow for low-level analysis of single-cell RNA-seq ...
scRNA-Seq pipelines
Here we forge the tools to analyze single cell RNA-Seq experiments. The analysis workflow is based on the Bioconductor packages scater and scran as well as the Bioconductor workflows by Lun ATL, McCarthy DJ, & Marioni JC [*A step-by-step workflow for low-level analysis of single-cell RNA-seq ...