46 packages tagged with “biology”
Open source bioinformatics and computational biology toolbox written in F#.
Version of AForge Imaging Library used by Bio Library to support 16bit & 48bit images running on Windows, Mac, & Linux.
A .NET microscopy imaging application based on Bio library. Supports various microscopes by using imported libraries & GUI automation. Supported libraries include Prior® & Zeiss® & all devices supported by Micromanager 2.0 and python-microscope.
ISA compliant experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in the dotnet environment.
A .NET library & program for annotating, & editing various microscopy imaging formats using Bioformats supported images. including whole slide, pyramidal & series.
A .NET application & library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions. Supports Windows, Linux and Mac.
ARC helper functions for filesystem management.
A GUI-less version of Bio .NET library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions. Supports Windows, Linux and Mac.
ARC helper functions for Common workflow language.
ARC helper functions for contracts management.
Library for management of Annotated Research Contexts (ARCs) using an in-memory representation and runtime agnostic contract systems.
Cross platform Windows, Linux & Mac .NET10 bindings for OpenSlide(https://openslide.org/), including DeepZoomGenerator
BioFSharp.IO contains read/write functions for a diverse set of biological file formats such as Fasta, FastQ, GeneBank or GFF, as well as helper function for searching on or transforming the input data
Excel File IO methods for ISA compliant experimental metadata toolkit in F#. The underlying datamodel can be directly read from and written to ISA-Json and ISA-Excel (ISATab format) files.
A data model of the ARC concept via it's RO Crate profile
Fable compliant release for the ISA compliant experimental metadata toolkit in F#. Additionally to the compiled library, it is shipped with the uncompiled code.
ARC and ISA compliant experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in the dotnet environment.
Functional graph-library written in F#
An experimental .NET library for processing different types of biological sequences
ARC and ISA json compliant parser for experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in isa-json format.
ARC helper functions for Parsing YAML files.
Visualization extensions for ISA compliant experimental metadata toolkit in F#. This project helps visualize the experimental workflow described in the experiment metadata.
TMEA (Thermodynamically Motivated Enrichment Analysis) is a thermodynamically motivated approach to gene set enrichment analysis
Make your workflow ML ready with BioFSharp.ML. Currently contains helper functionf for CNTK and a pre-trained model we used in our publication about predicting peptide observability.
BioFSharp.BioContainers gives you the possibility to leverage containerized applications without leaving you F# environment. We build on the fondation of Docker.DotNet to programmatically access the the REST API on top of the docker daemon. We provide special functions to use with biocontainers, which is a standardized way to create containerized bioinformatic software.
GPU parallelized functions from BioFSharp
ARC and ISA xlsx compliant parser for experimental metadata toolkit in F#. This project is meant as an easy means to open, manipulate and save ISA (Investigation,Study,Assay) metadata files in isa-xlsx format.