Software

Schwartz Lab GitHub Repository

This is the lab's GitHub repository. In it, we deposit our main software, but also references to code developed by the lab members to do common tasks in biological data analysis.


Txtools

txtools is a package that processes RNA-seq reads alignments into transcriptomic-oriented tables (Garcia-Campos and Schwartz, 2024). Enabling a quick and simplified analysis, to closely inspect summarized RNA-seq data per transcript, at nucleotide resolution, i.e. coverage, read-starts, read-ends, deletions, and nucleotide frequency. Attractive plotting is also readily available to visualize data.


MAZTER-mine

MAZTER-mine is a computational pipeline to analyze MAZTER-seq derived data (Garcia-Campos et al., 2019), a methodology developed in our lab to profile m6A quantitatively across transcriptomes with a single-base resolution.

A tutorial along with test-data on how to use MAZTER-mine is also available in our lab’s GitHub repository.