stochasticsdrj

diffractsim

✨ A flexible diffraction simulator for exploring and visualizing physical optics.

Fringe.Py

A Python implementation of diffraction and coherent field propagation by angular spectrum method.

hypoquantyl

Image processing and analysis tool to measure growth kinematics of Arabidopsis seedlings

GrowthData

User Interface using R Shiny for the analysis of plant growth. The app is support RGB and Depth image sequences.

crystal-growth-rate-analysis

Python-based image processing scripts with an interactive GUI for extracting crystal growth rates from in situ microscopy images.

hypotrace

HYPOTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape

wire

:wavy_dash: Overview of the open source code for Wire

SOAPdenovo2

Next generation sequencing reads de novo assembler.

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

haslr

A fast tool for hybrid genome assembly of long and short reads

OPERA-MS

OPERA-MS - Hybrid Metagenomic Assembler

SIS

a program to generate draft genome sequence scaffolds for prokaryotes

sspace_basic

SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension

CSAR

A contig scaffolding tool using algebraic rearrangements.

VelvetOptimiser

:chart_with_upwards_trend: Automatically optimise three of Velvet's assembly parameters.

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

idep

Integrated Differential Expression and Pathway analysis

variant-calling-pipeline

HPC based pipelines for variant calling using GATK

psearch

3D ligand-based pharmacophore modeling

pmapper

3D pharmacophore signatures and fingerprints

apps-ambit

Applications using AMBIT and examples how to call AMBIT modules

fmcsR

Mismatch Tolerant Maximum Common Substructure Searching

protein-science

A collection of useful tutorials for Protein Science

Graph-Based-Molecular-Synthesis

Synthesis of molecules from fragments into larger molecules using graph-based representations and techniques.

eMolFrag

eMolFrag is a molecular fragmentation tool based on BRICS algorithm written in Python.

AutoCouple_Python-based

Python Scripts used within the AutoCouple methodology developped by the groups of Prof. Caflisch and Prof. Nevado

DeepNeuralNet-QSAR

nanopolish

Signal-level algorithms for MinION data