Transcriptomics Tools

R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

SPARK is an efficient method to identify genes with spatial expression pattern. The intended applications are spatially resolved RNA-sequencing from e.g. Spatial Transcriptomics, slide-seq, or in situ gene expression measurements from e.g. seqFISH, MERFISH.

Ultrafast universal RNA-seq data aligner.

An interactive and narrative visualisation tool for single-cell and spatial data.

A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.