Transcription factors and regulatory sites Tools

The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.

Model based analysis for chip-seq data

Identify transcription factor binding sites from ChIP-seq data at high resolution.

Fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.

Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature.

CellRank is a package for mapping the fate of single cells in diverse scenarios, including perturbations such as regeneration or disease, for which direction is unknown. The approach combines the robustness of trajectory inference with directional information from RNA velocity, derived from ratios of spliced to unspliced reads. CellRank takes into account both the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in RNA velocity vectors

CellRank is a package for mapping the fate of single cells in diverse scenarios, including perturbations such as regeneration or disease, for which direction is unknown. The approach combines the robustness of trajectory inference with directional information from RNA velocity, derived from ratios of spliced to unspliced reads. CellRank takes into account both the gradual and stochastic nature of cellular fate decisions, as well as uncertainty in RNA velocity vectors

A rapid, high-throughput, and variant-aware in silico off-target site identification for CRISPR genome editing. Tool package to perform in-silico CRISPR analysis and assessment. CRISPRitz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.