178 Open source projects that are alternatives of or similar to sunbeam

Strain-level abundances estimation in metagenomic samples using variation graphs

Live code in Pandoc Markdown

⛔ ARCHIVED ⛔

Avalanche: a End-to-End Library for Continual Learning.

Code for "Depth Uncertainty in Neural Networks" (https://arxiv.org/abs/2006.08437)

A Collection of Variational Autoencoders (VAE) in PyTorch.

[MIRROR] Emacs support for Snakemake

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

No description or website provided.

Lightweight, Python library for fast and reproducible experimentation 🔬

From genomes to phenotypes: Traitar, the microbial trait analyzer

R interface to the Open Science Framework (OSF)

Meta-Omics Software for Community Analysis

Everware is about re-useable science, it allows people to jump right in to your research code.

An easy-to-use way for running Galaxy workflows.

FMA: A Dataset For Music Analysis

Platform for integrating genomic analysis with Jupyter Notebooks.

This is our implementation of ENMF: Efficient Neural Matrix Factorization (TOIS. 38, 2020). This also provides a fair evaluation of existing state-of-the-art recommendation models.

Kervolution implementation using TF2.0

A platform for end-to-end development of machine learning solutions in biomedical imaging

A Deep Learning Approach to Ultrasound Image Recovery

An R package for storing and retrieving data.frames in git repositories.

Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

Statistical Analysis of RNA-Seq Tools

Remove contaminated contigs from genomes using k-mers and taxonomies.

Nozzle is a report generation toolkit for data analysis pipelines implemented in R.

📦 Create a package or compendium structure

☁️ 🚀 📊 📈 Evaluating state of the art in AI

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

Source code for the CERN Analysis Preservation portal

Framework for Analysis of Class-Incremental Learning with 12 state-of-the-art methods and 3 baselines.

Curated set of transformers that make your work with steppy faster and more effective 🔭

Empirical Software Engineering journal (EMSE) open science and reproducible research initiative

MEX Vocabulary: a lightweight machine learning interchange format

Reproducible R Scripts Via Date Controlled Installing & Loading of CRAN & Git Packages

Pytorch implementations of Bayes By Backprop, MC Dropout, SGLD, the Local Reparametrization Trick, KF-Laplace, SG-HMC and more

Cross-disease comparison of case-control gut microbiome studies

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

MaAsLin2: Microbiome Multivariate Association with Linear Models

Scientific reports/literate programming for Julia

The GenePattern Server web application

A research tool for the Iterated Prisoner's Dilemma

The uncompromising Snakemake code formatter

Presentation-Ready Data Summary and Analytic Result Tables

A library for creating and curating reproducible pipelines for scientific and industrial machine learning

papaja (Preparing APA Journal Articles) is an R package that provides document formats to produce complete APA manuscripts from RMarkdown-files (PDF and Word documents) and helper functions that facilitate reporting statistics, tables, and plots.

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

Experiments for understanding disentanglement in VAE latent representations

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Interactive Jupyter widgets to visualize images, point sets, and meshes in 2D and 3D

Close assembly gaps using long-reads at high accuracy.

Functional workflows

WRENCH: Cyberinfrastructure Simulation Workbench

🐍 Snakefiles for common RNA-seq data analysis workflows.

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

Best practices for applying machine learning to bacterial 16S rRNA gene sequencing data

Fully reproducible, open source scientific articles in LaTeX.

ukbREST: efficient and streamlined data access for reproducible research of large biobanks

Guide for Reproducible Research and Data Science in Jupyter Notebooks

Package an R workspace and all dependencies as a Docker container