637 Open source projects that are alternatives of or similar to gene-oracle

📊 Identify cell types and pathways affected by genetic risk loci.

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

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

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

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

API for linked biological knowledge

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

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

GRAph-based Finding of Individual Motif Occurrences

📊 Codon usage tables in code-friendly format + Python bindings

Golang for Bioinformatics

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Train PyTorch Models using the Genetic Algorithm with PyGAD

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

The BridgeDb Library source code

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

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

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

GNparser normalises scientific names and extracts their semantic elements.

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Use genetic algorithms to train flappy bird

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

An R package for reproducible and automated ADMIXTOOLS analyses

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

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

Classify sequencing reads using MinHash.

This repository belongs to the youtube videos "What are Genetic Algorithms" (https://youtu.be/uQj5UNhCPuo) and "Genetic Algorithm from Scratch in Python" (https://youtu.be/nhT56blfRpE). If you haven't seen it, please consider watching part one of this series, to get a better understanding of this code.

Single Cell Analysis Pipelines

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

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

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Read and write FASTQ and FASTA efficiently from Python

FMI-compliant Model Estimation in Python

Modern Fortran Edition of the Pikaia Genetic Algorithm

A permissively licensed library designed to replace Illumina's Experiment Manager

🎯 Human transcription factor target genes.

Genomics using open source tools, running on GCP or AWS

Open source Java library for computational proteomics

Go evolutionary algorithm is a computer library for developing evolutionary and genetic algorithms to solve optimisation problems with (or not) many constraints and many objectives. Also, a goal is to handle mixed-type representations (reals and integers).

FEELnc : FlExible Extraction of LncRNA

Toolkit for preparing genomes for submission to NCBI

An R package for optimization using genetic algorithms

Ploidy agnostic phasing pipeline and algorithm

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Genetic Algorithms Toolbox

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.

zoofs is a python library for performing feature selection using a variety of nature-inspired wrapper algorithms. The algorithms range from swarm-intelligence to physics-based to Evolutionary. It's easy to use , flexible and powerful tool to reduce your feature size.

Computational Analysis of Novel Drug Opportunities

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

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Fast hash function for DNA sequences

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

The Ensembl Compara Perl API and SQL schema