Transposon Genomics Software
Software development in the Gale Hammell lab focuses on maximizing data recovery from high throughput sequencing projects. In particular, the lab is interested in improving bioinformatics analysis of transposable elements in order to recover these sequences from genomics profiling asssays. What new biology might be lurking in the transposon genomics realm?
We have developed the following tools to address various bioinformatics needs:
TEToolkit suite
TEtranscripts: A package for including transposable elements in differential expression analysis of sequencing datasets (RNA-seq).
TEsmall: A package for including small RNAs derived from repetitive regions in differential expression analysis (sRNA-seq).
TElocal: A package for quantifying transposable element expression at the locus level (RNA-seq).
TEsingle: A package for quantifying transposable elements from single-cell/nuclei RNA-seq datasets
Single-cells & Classifiers
CellRanger-TE: A method for including TEs in a standard CellRanger single-cell analysis (scRNA-seq/nuc-seq)
SAKE: A user-friendly tool for downstream analysis of single-cell RNA-seq data (clustering, plotting & differential expression).
DANCer: A package to classify ALS post-mortem cortex RNA-seq datasets into their molecular subtypes.
Choosing the right TE software
Handling transposon derived reads can be tricky. There are lots of software packages out there, but how do you pick the right one?
In this 2020 review, we describe all of the software that’s been developed for handling transposable elements in common genomics assays, such as: RNA-seq, ChIP-seq, CLIP-seq, DNA methyl-seq, and small RNA data. There’s also lots of room for improvement, both computationally and experimentally.
We hope this review will be helpful both to TE experts as well as newcomers to the transposon field.
