PIDE

Highly accurate prophage island detection with PIDE.

2026.06.0140

MAGdb

MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.

2026.06.0100

CrossExpression

Cross-expression meta-analysis of mouse brain slices reveals coordinated gene expression across spatially adjacent cells.

2026.06.0100

iPro-MP

iPro-MP: a BERT-based model to predict multiple prokaryotic promoters.

2026.06.0100

SpatPPI

SpatPPI: a geometric deep learning model for predicting protein-protein interactions involving intrinsically disordered regions.

2026.06.0100

ENGINE

A scalable equivariant graph network framework for precise protein function prediction.

2026.06.0100

ricePSP

ricePSP: a database of rice phase separation-associated proteins.

2026.06.0100

HUBMet

HUBMet: an integrative database and analytical platform for human blood metabolites and metabolite-protein associations.

2026.06.0100

PoreOver

Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing.

2026.05.2200

GWAS-VCF

The variant call format provides efficient and robust storage of GWAS summary statistics.

2026.05.2200

SIAMCAT

Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.

2026.05.2200

scMET

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution.

2026.05.2200

gapseq

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.

2026.05.2200

seqQscorer

seqQscorer: automated quality control of next-generation sequencing data using machine learning.

2026.05.2200

2passtools

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.

2026.05.2200

Samplot

Samplot: a platform for structural variant visual validation and automated filtering.

2026.05.2200

nPhase

nPhase: an accurate and contiguous phasing method for polyploids.

2026.05.2200

INFIMA

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants.

2026.05.2220

Easy-Prime

Easy-Prime: a machine learning-based prime editor design tool.

2026.05.2200

Flimma

Flimma: a federated and privacy-aware tool for differential gene expression analysis.

2026.05.2200

recount3

recount3: summaries and queries for large-scale RNA-seq expression and splicing.

2026.05.2200

DNA methylation database

DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation.

2026.05.2200

AGAMEMNON

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite.

2026.05.2200

CellPhy

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data.

2026.05.2200

Network of Cancer Genes (NCG)

Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource.

2026.05.2200

sPLINK

sPLINK: a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies.

2026.05.2200

GENEVA

Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

2026.05.2200

FORGE2

Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.

2026.05.2200

JAFFAL

JAFFAL: detecting fusion genes with long-read transcriptome sequencing.

2026.05.2200

Chronos

Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects.

2026.05.2200

SHOOT

SHOOT: phylogenetic gene search and ortholog inference.

2026.05.2200

TraSig

TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data.

2026.05.2200

HiCBin

HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps.

2026.05.2200

scCCESS

Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data.

2026.05.2200

diffnet

Dynamic rewiring of biological activity across genotype and lineage revealed by context-dependent functional interactions.

2026.05.2200

PEKA

Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP.

2026.05.2100

Prokounter

Differential richness inference for 16S rRNA marker gene surveys.

2026.05.2100

scSTEM

scSTEM: clustering pseudotime ordered single-cell data.

2026.05.2100

MMUPHin

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin.

2026.05.2100

SIEVE

SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data.

2026.05.2100