TFscope
Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they orchestrate gene expression. TFscope is a machine learning approach that identifies sequence features explaining the binding differences observed between two ChIP-seq experiments targeting either the same TF in two conditions or two TFs with similar motifs (paralogous TFs). TFscope systematically investigates differences in the core motif, nucleotide environment and co-factor motifs, and provides the contribution of each key feature in the two experiments.
TFscope online execution
Other tools
EPIK
Precise and scalable evolutionary placement with informative k-mers EPIK is a program dedicated to « Phylogenetic Placement » (PP) of metagenomic or metabarcoding reads on a reference tree. It is similar in spirit and technically the successor of RAPPAS (Linard et al. 2020). EPIK achieves identical or slightly better accuracy than RAPPAS and outperforms it in speed and…
WAVES
Summary WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order…
TIDE
What is TIDE? TIDE is the orchestration platform behind ATGC online bioinformatics services. It provides a unified web interface and a public REST API to submit analyses, monitor jobs, and retrieve results across a growing catalog of phylogenetic and sequence-analysis tools. TIDE is a modernized redesign of WAVES, an older tool previously developped by ATGC…