489 Open source projects that are alternatives of or similar to BioKEEN

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Simple pure Python SAM parser and objects for working with SAM records

Mulled - Automatized Containerized Software Repository

A package for designing compact and comprehensive capture probe sets.

Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

Fast hash function for DNA sequences

An open-access bioinformatics text

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Compute N50/NG50 and auN/auNG

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

Improving genome bins through the combination of different binning programs

Fast and flexible ORF finder

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

My own tools code for NGS data analysis (Next Generation Sequencing)

Read and write FASTQ and FASTA efficiently from Python

A Python platform for Structural Bioinformatics

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

Provide R access to the NCI Genomic Data Commons portal.

Cyber-investigation Analysis Standard Expression (CASE) Ontology

Transformation du répertoire SIRENE (CSV) au format RDF pour publication en Linked Data

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Open Source Decentralized Identifiers and Verifiable Credentials Infrastructure and Tooling

CubiQL: A GraphQL service for querying multidimensional Linked Data Cubes

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

Version 5 of the CAFE phylogenetics software

An R package for reproducible and automated ADMIXTOOLS analyses

A curated list of ontology things

Feature extraction algorithm for genomic data

GWAS summary statistics files QC tool

🎯 Human transcription factor target genes.

Bystro genetic analysis (annotation, filtering, statistics)

Ploidy agnostic phasing pipeline and algorithm

Assembling the cause of phenotypes and genotypes from NGS data

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

SPARQL micro-services: A lightweight approach to query Web APIs with SPARQL

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Rapid determination of appropriate reference genomes.

API for linked biological knowledge

Method to optimally select samples for validation and resequencing

Golang for Bioinformatics

A suite of LDP software and middleware for RDF.rb & Rack

A Kotlin DSL and library to create and plot RNA 2D structures

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

A fast and lightweight streaming JSON-LD serializer for JavaScript

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

Open source Java library for computational proteomics

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Stacked Denoising AutoEncoder based on TensorFlow

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

MView extracts and reformats the results of a sequence database search or multiple alignment.

Streamlining SLAM-seq analysis with ultra-high sensitivity

Unsupervised domain adaptation method for relation extraction

A curated list of resources for machine learning for small-molecule drug discovery

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Useful bioinformatic scripts

3D printed sculpture of a DNA molecule, showing my own genome

WebGL Heatmap Viewer for Big Data and Bioinformatics