Terkko Navigator / Bioinformatics (journal)

MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data

BLANT—fast graphlet sampling tool

scRNABatchQC: multi-samples quality control for single cell RNA-seq data

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers

Sequence tube maps: making graph genomes intuitive to commuters

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

PyMethylProcess—convenient high-throughput preprocessing workflow for DNA methylation data

MPRAscore: robust and non-parametric analysis of massively parallel reporter assays

CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models

Predicting promoters in phage genomes using PhagePromoter

DISPOT: a simple knowledge-based protein domain interaction statistical potential

geneCo: a visualized comparative genomic method to analyze multiple genome structures

The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets

amplimap: a versatile tool to process and analyze targeted NGS data

TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets

SquiggleKit: a toolkit for manipulating nanopore signal data

diSTruct v1.0: generating biomolecular structures from distance constraints

sAOP: linking chemical stressors to adverse outcomes pathway networks

Genetic association testing using the GENESIS R/Bioconductor package

PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities

VariantQC: a visual quality control report for variant evaluation

DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis

MEpurity: estimating tumor purity using DNA methylation data

MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees

HDX-Viewer: interactive 3D visualization of hydrogen–deuterium exchange data

VeriNA3d: an R package for nucleic acids data mining

ValTrendsDB: bringing Protein Data Bank validation information closer to the user

The NEW ESID online database network

CytoGPS: a web-enabled karyotype analysis tool for cytogenetics

Benchmarking fold detection by DaliLite v.5

RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons

JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis

Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages

Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers

TCR3d: The T cell receptor structural repertoire database

Interactive exploration of heterogeneous biological networks with Biomine Explorer

CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data

A fully computational and reasonable representation for karyotypes

KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules

DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network

DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data

A scalable method for parameter identification in kinetic models of metabolism using steady-state data

Graphlet Laplacians for topology-function and topology-disease relationships

New algorithms for detecting multi-effect and multi-way epistatic interactions

Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms

MTTFsite: cross-cell type TF binding site prediction by using multi-task learning

AutoDock CrankPep: combining folding and docking to predict protein–peptide complexes

DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures