Thomas's repositories
streamlit-example
Example Streamlit app that you can fork to test out share.streamlit.io
GeneULike
Repository for gene lists
GeneULike-1
GeneULike
reproGenomicsViewer
The ReproGenomics Viewer is a cross-species genomic resource for the reproductive science community. It aims to centralize and harmonize ultra-high-throughput sequencing data accumulated in the field of reproductive biology and to assist scientists in the exploration of these datasets.
toxsign_v2
The TOXicogenomic sIgNature (TOXsIgN) is a user-friendly and cross-species resource that supports online submission, storage, and retrieval of TOXicogenomic sIgNatures. TOXsIgN aims at complementing existing resources by acting as a distribution hub for the community. One of its unique features is its ability to archive heterogeneous data.
TOXsIgN
The TOXicogenomic sIgNature (TOXsIgN) repository provides a flexible and open design that facilitates online submission by the toxicology community, storage and retrieval of toxicogenomic signatures, defined as the description of (transcript-/epigen-)omics effects on individuals or their descendants, after exposure to single or combined environmental factors, including chemical (e.g. pesticides, plasticizers, drugs, endocrine disruptors), physical (e.g. radiations, temperature) or biological (e.g. pathogens, parasites) factors. TOXsIgN also intends to serve as a warehouse for toxicogenomics and predictive toxicology tools which could lean on the deposited signatures deposited by the community.
RGV
The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community. The system is based on the implementation of a JBrowse genome browser and a Galaxy bioinformatics workflow environment. It was developed to provide a one-stop genomic working environment and aims to assist scientists in the analysis and the mining of a wide range of high-throughput repro-genomics data, including sequencing data. RGV allows hosting, visualization, and direct comparison of users’ data to published genomics studies as well as to relevant genetic variations linked to reproduction. One way it does this is by enabling various genomic file format conversions. The ReproGenomics Viewer currently hosts datasets that are oriented mainly towards testis biology and spermatogenesis. In the near future, these will extend to other areas of reproduction, including gonad development, urogenital cancers, and reproductive toxicology. If you use RGV please cite : Darde et al. , Nucleic Acids Res., 2015 Jul
ChemPSy
Chemical Prioritization System - ChemPSy The aim of **ChemPSy** (Chemical Prioritization System) is to develop an innovative approach based on several bioinformatics and biostatistics methodologies to analyze and integrate massive toxicogenomics datasets. Specific objectives include: (1) classification of chemicals based on transcriptional signatures, e.g. the set of genes whose expression is known to be positively or negatively altered after an exposure to these compounds; (2) the association of classes with human pathologies or deleterious phenotypes, e.g. classes containing toxicants with well-known effects; (3) the prediction of novel reprotoxicants and/or endocrine disruptors based on transcriptional signature similarities with known chemicals affecting testis development and function.
NYRA2018
Event webpage of NYRA2018 meeting
convertToEntrezGeneID
Download biological databas, extract database identifier and entrez gene identifier, insert in a mongo database