mitoSplitter – A mitochondrial variants-based method for efficient demultiplexing of pooled single-cell RNA-seq
Single-cell RNA-seq (scRNA-seq) analysis of multiple samples separately can be costly and lead to batch…
Browsing: Analysis Pipelines
SAHMI – denoising sparse microbial signals from single-cell sequencing of mammalian host tissues
Existing genomic sequencing data can be used to study host–microbiome ecosystems; however, distinguishing signals that…
A cross-cohort computational framework to trace tumor tissue-of-origin based on RNA sequencing
Carcinoma of unknown primary (CUP) is a type of metastatic cancer with tissue-of-origin (TOO) unidentifiable…
ScRNAPip – A systematic and dynamic pipeline for single-cell RNA sequencing analysis
With the advancement of sequencing technology, cell separation, and whole-genome amplification techniques, single cell technology…
TimeTalk – decipher cell-cell communication from single-cell RNA-seq datasets
Early embryonic development is a dynamic process that relies on proper cell-cell communication to form…
scProjection – projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles
Multi-modal single cell RNA assays capture RNA content as well as other data modalities, such…
iDESC – identifying differential expression in single-cell RNA sequencing data with multiple subjects
Single-cell RNA sequencing (scRNA-seq) technology has enabled assessment of transcriptome-wide changes at single-cell resolution. Due…
Interactive analysis of single-cell data using flexible workflows with the Single-Cell Toolkit 2
Analysis of single-cell RNA sequencing (scRNA-seq) data can reveal novel insights into the heterogeneity of…
METAFlux – infer metabolic fluxes from bulk or single-cell transcriptomic data
Cells often alter metabolic strategies under nutrient-deprived conditions to support their survival and growth. Characterizing…
MSIQ -joint modeling of multiple RNA-seq samples for accurate isoform quantification
Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance…