Resources
HSPC Classifier
We developed a machine learning classifier to annotate human hematopoietic stem and progenitor cell (HSPC) populations from bone marrow single-cell RNA-seq data. This tool can be used to annotate your scRNA-seq data based on cell types identified in our prior work.
LSC Reference
Using single-cell multi-omics, were able to identify AML LSCs at high resolution and purity. We developed an integrated single cell data set and reference signature matrix for bulk gene expression deconvolution as part of this study. The methods used to generate these tools are provided here.
Xenotransplantation Protocol
Protocol describing intrafemoral injection of hematopoietic or leukemic stem cells, including gene-edited cells, in murine xenograft models, which will not only enable the quick and safe transplantation of cells but also serial analyses of the bone marrow. The protocol is published here.
PrismR
PrismR is a R Shiny app for plotting and statistics. It uses the ggprism theme and palettes for visual parity with Prism, and exposes R’s statistical framework through rstatix. The interface is highly customizable with plotting and statistics options similar to GraphPad Prism with added 3D plotting capabilities.
GenAnalysis
GenAnalysis is an open-source, native genomic-engineering workbench for macOS and iPadOS, built in Swift. It includes a gene browser (Ensembl REST), primer design, CRISPR guide design, an IGV-style BAM viewer, and NCBI BLAST sequence search.