Software

RNAGlib: a library to manipulate RNA structural data. RNAglib also includes a benchmarking facility with a set of tasks and metrics on RNA structure-function relationship.
CrAI: CrAI is a lightweight tool to predict the location of antibodies in cryo-EM maps. It is available as as ChimeraX plugin
RNAmigos: an RNA virtual screening tool, available on Google Colab.
quickSOM: a GPU-based implementation of the Self-Organising Maps algorithms, with support for Jax or Pytorch backends.
Komet: a Kronecker-optimized method for drug-target interaction prediction
PyCombat: a Python implementation of ComBat for batch effects correction
gwas-tools: discover susceptibility genes in GWAS using network-guided approaches
MuGLasso GWAS: multitask group lasso to analyze GWAS data across diverse populations
kernelPSI: Post-selection inference with kernels
epiGWAS: Robust methods for epistasis detection
martini: GWAS incorporating networks in R (includes SConES)
ZINBWaVE: Zero-Inflated Negative Binomial based Wanted Variation Extraction
HiC-Pro : An optimized and flexible pipeline for Hi-C processing
[PASTIS]: Poisson-based Algorithm for STable Inference of DNA Structure
[FlipFlop]: Fast Lasso-based Isoform Prediction as a Flow Problem
[TIGRESS]: Trustful inference of gene regulation using stability selection
[ProDiGe]: Prioritization of disease genes
[GFLseg]: Group fused lasso for signal segmentation
[ClusterPath]: Clustering using convex fusion penalties
[FREEC]: Control-FREE Copy number caller from deep-sequencing data
[GraphM]: Graph matching package
[PARIS]: Pocket Alignment in Relation to Identification of Substrates
[SIRENE]: Supervised Inference of REgulatory NEtwork
[KISS]: MHC-I epitope prediction
[GAkernel]: Global alignment kernel for time series comparison
[DSIR]: design of siRNA
[ChemCpp]: a C++ toolbox for chemoinformatics integrating the computation of kernels functions between chemical compounds
[SLP-Local]: prediction of protein subcellular localization from their amino-acid sequence with support vector machines
[NGrid]: open source grid computing framework