OrientAGraph

Advancing admixture graph estimation via maximum likelihood network orientation.

2026.05.15100

APAtizer

APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data.

2025.12.0410

spatialMNN

Spatial mutual nearest neighbors for spatial transcriptomics data.

2025.12.0300

ReAlign-P

ReAlign-P: A vertical iterative realignment method for protein multiple sequence alignment.

2025.12.0300

dmGsea

Efficient gene set analysis for DNA methylation addressing probe dependency and bias.

2025.12.0300

jMF2D

Enhancing and accelerating cell type deconvolution of large-scale spatial transcriptomics slices with dual network model.

2025.12.0300

AF3Complex

AF3Complex Yields Improved Structural Predictions of Protein Complexes.

2025.12.0300

RNAgg

Deep generative model of RNAs based on variational autoencoder with context free grammar.

2025.12.0300

2OMe-LM

2OMe-LM: predicting 2'-O-methylation sites in human RNA using a pre-trained RNA language model.

2025.12.0300

Prot2Chat

Prot2Chat: Protein LLM with Early-Fusion of Text, Sequence and Structure.

2025.12.0320

UCSCXenaShiny1.1.5

UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data

2022.01.28281

WHdenovo

A haplotype-Aware de novo assembly of related individuals using pedigree sequence graph

2022.01.1980

Ribotricer

Accurate detection of short and long active ORFs using Ribo-seq data

2022.01.1980

Prodigy

PRODIGY: Personalized prioritization of driver genes

2022.01.1980

DeepPPISP

Protein-protein interaction site prediction through combining local and global features with deep neural networks

2022.01.19100

IntegratedPhasing

Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes

2022.01.1980

SynergyFinder1.0.0

SynergyFinder: A web application for analyzing drug combination dose-response matrix data

2022.01.1990

XPN

Merging two gene-expression studies via cross-platform normalization

2022.01.1980

isoMiRmap

IsoMiRmap: Fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets

2022.01.19100

DeepSELEX

DeepSELEX: Inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs

2022.01.1980

UTRannotator

Annotating high-impact 5?€?untranslated region variants with the UTRannotator

2022.01.1980

viaDBG

Inference of viral quasispecies with a paired de bruijn graph

2022.01.1980

WFA

Fast gap-affine pairwise alignment using the wavefront algorithm

2022.01.1990

HiSCF

HiSCF: Leveraging higher-order structures for clustering analysis in biological networks

2022.01.1980

VEGA ZZ

The VEGA suite of programs: An versatile platform for cheminformatics and drug design projects

2022.01.19110

KOBT

Knockoff boosted tree for model-free variable selection

2022.01.1980

SAAMBE-SEQ

SAAMBE-SEQ: A sequence-based method for predicting mutation effect on protein-protein binding affinity

2022.01.1980

CSynth

CSynth: An interactive modelling and visualization tool for 3D chromatin structure

2022.01.1980

CABEAN

CABEAN: A software for the control of asynchronous Boolean networks

2022.01.1980

KORP-PL

KORP-PL: A coarse-grained knowledge-based scoring function for protein-ligand interactions

2022.01.19110

ViralMSA

ViralMSA: Massively scalable reference-guided multiple sequence alignment of viral genomes

2022.01.1980

CLoNe

CLoNe: Automated clustering based on local density neighborhoods for application to biomolecular structural ensembles

2022.01.19100

CoV-AbDab

CoV-AbDab: The coronavirus antibody database

2022.01.19100

ipDMR

IpDMR: Identification of differentially methylated regions with interval P-values

2022.01.1980

SAIGEgds

SAIGEgds - An efficient statistical tool for large-scale PheWAS with mixed models

2022.01.1980

minMLST

minMLST: machine learning for optimization of bacterial strain typing

2022.01.1980

SASC

Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses

2022.01.1990

GraphQA

GraphQA: protein model quality assessment using graph convolutional networks

2022.01.1980

BSAseq

BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations

2022.01.1990

iCarPS

ICarPS: A computational tool for identifying protein carbonylation sites by novel encoded features

2022.01.19100