software / tool

GlycoDiveR provides a modular R framework for analyzing and visualizing high-dimensional glycoproteomics data, improving accessibility and flexibility in glycosylation analysis.

This study identifies cellular stress tolerance as a key factor in genetic transformability of Candida species and develops a method to improve CRISPR screening efficiency.

Prosculpt is a protein design pipeline that simplifies the use of multiple tools for protein design, enabling users to perform complex tasks without coding.

The paper develops LongAIRR, a computational framework for spatially resolving adaptive immune receptor repertoires from long-read sequencing, improving consensus accuracy and enabling platform-agnostic analysis.

CREPAS is a Nextflow pipeline for analyzing nascent chromatin sequencing data, improving scalability, reproducibility, and compatibility across multiple chromatin assays.

fastder detects expressed regions from RNA-seq data without relying on annotations, achieving high accuracy and speed for large-scale analysis.

ParTIpy scales archetypal analysis for biological trade-offs and integrates with single-cell workflows, enabling task inference in large datasets.

kmerRRR improves analysis of repetitive genomic regions by using k-mer frequency analysis to enhance mappability and recover lost biological signals in chromatin and small RNA data.

Bamsnap-LRS automates batch visualization of long-read sequencing alignments, supporting genomic, transcriptomic, and haplotype-aware analyses with publication-ready figure generation.

PepMCP predicts membrane contact probability for short peptides using graph-based modeling, achieving high correlation with experimental data.

EnrichViz provides an interactive R Shiny tool for visualizing pathway enrichment results from omics data without requiring coding.

MLMarker computes tissue similarity scores for proteomics data, identifies tissue origins in biofluids, and provides interpretable predictions using a Random Forest model.

qPCR Guru provides a platform for improved qPCR analysis by comparing instrument-derived and full-curve Cq estimates, enhancing accuracy for low-expressing targets.

The paper develops a multi-model consensus deep learning approach for automated gold fiducial marker segmentation in prostate MRI, achieving high sensitivity and precision.

This paper introduces Proto, a high-level programming language for generative biology, and demonstrates its use in designing and validating biological systems.

The paper evaluates 54 tick genome assemblies, identifies 34 high-quality ones, and recommends long-read sequencing and Hi-C scaffolding to improve tick genomic resources.

DiaReport provides a reproducible workflow for differential expression analysis and interactive reporting in DIA-based proteomics, demonstrating its utility with an extracellular vesicle dataset.

EMAlign improves cryo-EM map alignment using deep learning to predict main-chain probability, achieving high accuracy and success rates across global and local alignments.

ResXR provides an open-source toolkit for reproducible human behavior studies in Extended Reality, converting immersive experiments into standardized datasets with quality reports.

HoloBio provides an open-source software tool for analyzing holographic microscopy data, supporting real-time and offline processing with features for cell tracking and morphological analysis.

Accelign accelerates pairwise sequence alignment using GPUs, achieving significant speedups over existing CPU and GPU implementations for DNA, RNA, and protein sequences.

The paper introduces scVizComm, a web tool for visualizing cell-cell communication in single-cell transcriptomics data with pathway-centric prioritization.

XVCF provides a user-friendly GUI tool for visualizing and analyzing VCF data from genomic experiments, offering quality control metrics and interactive exploration of genetic variants.

SenoQuant is an AI software for analyzing and predicting senescence markers in tissues, offering spatial quantification across imaging modalities and supporting custom models.

Ovo provides an open-source platform for de novo protein design, integrating tools, workflows, and visualization to simplify and scale the design process.

The recount3 Python package provides programmatic access to uniformly processed RNA-seq data, enabling efficient use in Python-based computational pipelines.

Biom3d is a modular deep learning framework for 3D image segmentation that improves code sustainability and reproducibility.

This paper introduces an autonomous AI agent that performs scientific research tasks end-to-end, demonstrating its ability to generate research artifacts and expose pipeline dynamics.

LT-FGRS estimates genetic liabilities from large-scale family data, unifying methods into an R package for efficient population-scale analysis.

This paper shows that task engagement in fMRI reorganizes infra-slow BOLD dynamics by redistributing power across frequencies rather than just adding to ongoing activity.