569 Open source projects that are alternatives of or similar to Octopus

The START App: R Shiny Transcriptome Analysis Resource Tool

Fast and flexible ORF finder

Toolkit for processing sequences in FASTA/Q formats

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

Aggregate results from bioinformatics analyses across many samples into a single report.

Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

Mulled - Automatized Containerized Software Repository

MISO: An open-source LIMS for NGS sequencing centres

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

The uncompromising Snakemake code formatter

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

Global Biotic Interactions provides access to existing species interaction datasets

WebGL Heatmap Viewer for Big Data and Bioinformatics

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

Version 5 of the CAFE phylogenetics software

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Sample search by metadata and features

🎯 Human transcription factor target genes.

Characterization of Germline variants

Ploidy agnostic phasing pipeline and algorithm

C library for high-throughput sequencing data formats

Create regional association plots from GWAS or meta-analysis

A D library for computational biology and bioinformatics

Biostar Q&A

WebLogo 3: Sequence Logos redrawn

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Post-analysis of immune repertoire sequencing data

Exact Tandem Repeat Finder (not a TRF replacement)

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

echt rapid variant annotation and filtering

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Versatile open-source tool for microbiome analysis

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

A collaboratively written review paper on deep learning, genomics, and precision medicine

GeneValidator: Identify problems with predicted genes

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

Open source Java library for computational proteomics

Workflow Description Language - Specification and Implementations

An interactive web portal for exploring immuno-oncology data

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

Parser and database to index the terpene profile of different strains of Cannabis from online databases

An R package for reproducible and automated ADMIXTOOLS analyses

A cross-platform command-line tool for executing jobs in parallel

PERF is an Exhaustive Repeat Finder

✏️ A versatile DNA sequence optimizer

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

The Microbiome Interpretable Temporal Rule Engine

DOM Text Based Multiple Sequence Alignment Library

A simplified pipeline for ctDNA sequencing data analysis

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

MMseqs2 app to run on your workstation or servers

De novo genome assembly and multisample variant calling

Python module for average nucleotide identity analyses

Bioinformatics Workbook repository