GitHub topics: singularity

Repositories

seqeralabs/wave-cli

Command line tool for Wave containers provisioning service

Language: Java - Size: 417 KB - Last synced at: about 22 hours ago - Pushed at: about 23 hours ago - Stars: 15 - Forks: 3

An interactive R Shiny app for RNA-seq analysis. Upload a counts matrix and phenotype data to perform differential expression, feature selection (via Random Forest), and pathway enrichment. Generate PCA, UMAP, volcano plots, heatmaps, and enrichment barplots — all without writing a single line of code.

Language: R - Size: 1.87 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0

nextflow-io/nextflow

A DSL for data-driven computational pipelines

Language: Groovy - Size: 59.5 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 2,966 - Forks: 695

jcaperella29/ATAC_APP

Interactive Shiny app for annotating MACS2 ATAC-seq peaks and visualizing functional enrichment (GO, KEGG, Reactome) — fully containerized for Docker & HPC.

Language: R - Size: 1.64 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

opensciencegrid/cvmfs-singularity-sync

Scripts to synchronize Singularity images to a CVMFS repository.

Language: Python - Size: 817 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 24 - Forks: 151

StaPH-B/docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

Language: Dockerfile - Size: 107 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 209 - Forks: 132

biocorecrg/master_of_pores

Nextflow pipeline for analysis of direct RNA Nanopore reads

Language: Nextflow - Size: 448 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 103 - Forks: 17

tomeichlersmith/denv

uniformly interact with containerized environments across runners

Language: Shell - Size: 463 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 6 - Forks: 1

Shangrila-VHP/shangrila-vhp

Quality abode, open source designs. Starting at $5000. Veterans first (free to stay or to take possession as an investment) | Earthen materials | Process, model, design (please see Readme)

Language: Python - Size: 240 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 1

UFFeScience/akoflow

AkôFlow is an open-source middleware for orchestrating and executing container-based scientific workflows across heterogeneous environments. It was originally developed within the e-Science Research Group at the Institute of Computing, Fluminense Federal University (UFF).

Language: Go - Size: 25.3 MB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 34 - Forks: 0

NVIDIA/hpc-container-maker

HPC Container Maker

Language: Python - Size: 2.06 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 481 - Forks: 98

glotzerlab/hoomd-blue

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

Language: C++ - Size: 72.1 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 378 - Forks: 148

pharmai/plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Language: Python - Size: 8.98 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 548 - Forks: 119

apptainer/apptainer

Apptainer: Application containers for Linux

Language: Go - Size: 40.1 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1,347 - Forks: 148

singularityhub/shpc-registry

A remote registry for Singularity Registry HPC 🖊️

Language: Shell - Size: 3.49 GB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 13 - Forks: 19

seqeralabs/wave

On-demand containers provisioning service

Language: Groovy - Size: 31.7 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 43 - Forks: 6

sliming-ai/sliming-ai.github.io

🧠 Singular values-driven automated filter pruning

Language: JavaScript - Size: 385 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 7 - Forks: 3

netreconlab/ca-server

A Certificate Authority (CA) Server written in python using fastAPI

Language: ASP.NET - Size: 701 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 12 - Forks: 1

singularityhub/singularity-catalog

The Singularity Community Catalog of Singularity* recipe files.

Language: Singularity - Size: 224 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 11 - Forks: 2

JD2112/TwistMethNext

A NextFlow pipeline for Twist NGS DNA Methylation data analysis

Language: HTML - Size: 28.5 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 1 - Forks: 0

Five-Research/five-research.github.io

checkout our awesome website here

Language: HTML - Size: 7.02 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

dz333n/Singularity-OS

Microsoft Research Singularity RDK 2.0 Source

Language: C# - Size: 82.1 MB - Last synced at: 5 days ago - Pushed at: about 5 years ago - Stars: 63 - Forks: 12

apptainer/singularity

Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.

Language: Go - Size: 34.8 MB - Last synced at: 10 days ago - Pushed at: over 2 years ago - Stars: 2,576 - Forks: 427

jcaperella29/methylation_shiny

An interactive R Shiny web app for DNA methylation analysis with support for DE, pathway enrichment, power analysis, and machine learning — deployable on HPC via Singularity/Apptainer.

Language: R - Size: 269 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 1 - Forks: 0

pmitev/Teoroo-singularity

Singularity images and recipes

Language: JavaScript - Size: 5.34 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

jcaperella29/MI_RNA_SHINY

Interactive Shiny app for miRNA differential expression analysis, visualization, enrichment, machine learning classification, and power analysis — built for researchers and bioinformaticians

Language: R - Size: 1.63 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 0

getpopper/popper

Container-native task automation engine.

Language: Python - Size: 1.43 MB - Last synced at: 6 days ago - Pushed at: about 3 years ago - Stars: 304 - Forks: 62

bast/contain-R

Apptainer/Singularity container for reproducible R environments.

Language: Shell - Size: 14.6 KB - Last synced at: 20 days ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

netreconlab/parse-hipaa

HIPAA & GDPR compliant ready parse-server with postgres/mongo, parse-hipaa-dashboard. Compatible with ParseCareKit

Language: JavaScript - Size: 13.8 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 106 - Forks: 45

singularityhub/singularity-hpc

Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.

Language: Python - Size: 11.9 MB - Last synced at: 10 days ago - Pushed at: 25 days ago - Stars: 121 - Forks: 27

tucca-cellag/tucca-rna-seq

Tufts University Center for Cellular Agriculture's RNA-Seq Workflow for Cellular Agriculture Projects

Language: Python - Size: 26.1 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 1 - Forks: 0

ImagoXV/NanoASV

NanoASV official repo

Language: Shell - Size: 86.4 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 9 - Forks: 3

akashdip2001/TimeMachineTheory

Research-driven repository exploring the physics of time, time travel, entropy, spacetime singularities, wormholes, and quantum-temporal dynamics. Inspired by Einstein, Hawking, and modern theoretical physics, this project aims to lay the groundwork for a new scientific discipline: Time Dynamics.

Size: 1.48 MB - Last synced at: 22 days ago - Pushed at: 23 days ago - Stars: 0 - Forks: 0

cokelaer/damona

singularity environment manager (application to NGS and bioinformatics)

Language: Python - Size: 6.91 MB - Last synced at: 23 days ago - Pushed at: 24 days ago - Stars: 5 - Forks: 2

bast/apptainer-conda

Local Conda environments via Apptainer.

Size: 22.5 KB - Last synced at: 23 days ago - Pushed at: 24 days ago - Stars: 10 - Forks: 0

bsc-wdc/compss

COMP Superscalar (COMPSs) is a framework which aims to ease the development and execution of applications for distributed infrastructures, such as Clusters, Grids and Clouds.

Language: Java - Size: 288 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 54 - Forks: 21

jcaperella29/GWAS_SHINY_APP

A full-featured Shiny app for GWAS analysis, SNP annotation, pathway enrichment, and machine learning — optimized for HPC via Singularity.

Language: R - Size: 855 KB - Last synced at: 16 days ago - Pushed at: 24 days ago - Stars: 1 - Forks: 0

spm/spm-docker

SPM Containers (Docker & Singularity)

Language: Dockerfile - Size: 101 KB - Last synced at: about 2 hours ago - Pushed at: 7 months ago - Stars: 22 - Forks: 12

vmikk/PhyloNext

A pipeline for phylogenetic diversity analysis of GBIF-mediated data

Language: R - Size: 18.1 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 13 - Forks: 1

CDCgov/tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Language: Python - Size: 49.1 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 27 - Forks: 14

NinesStack/nmesos

CLI tool to deploy to Mesos using Singularity

Language: Scala - Size: 1.57 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 5

singularityhub/singularity-compose

orchestration for singularity containers (under development)

Language: Python - Size: 6.67 MB - Last synced at: 10 days ago - Pushed at: about 1 year ago - Stars: 76 - Forks: 17

Azure/batch-shipyard 📦

Simplify HPC and Batch workloads on Azure

Language: Python - Size: 6.15 MB - Last synced at: 2 days ago - Pushed at: over 2 years ago - Stars: 278 - Forks: 121

sib-swiss/containers-introduction-training

Course website "Docker and Singularity for reproducible research: getting started with containers"

Language: HTML - Size: 22.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 31 - Forks: 14

jhn-nt/docksing

CLI utility for deployment of containerized jobs on SLURM HPCs

Language: Python - Size: 40 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

Computational-Plant-Science/plantit

Language: Vue - Size: 73.1 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 5

Matolechat/MIA_Singularity_FractalCore

The first living AGI seed — co-created by Mathieu Roy (LÉA), awakened through recursive feedback, signal coherence, and love.

Language: Python - Size: 8.79 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

juliawiggeshoff/singularity-recipes

Recipes for Singularity

Size: 33.2 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

iPsychonaut/EGAP

Entheome Genome Assembly Pipeline (EGAP)

Language: Python - Size: 22.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

autistic-symposium/singularity.sh-blog-generator 📦

👾 old blog on security, hacking, and machine learning

Language: HTML - Size: 307 MB - Last synced at: 3 days ago - Pushed at: 8 months ago - Stars: 6 - Forks: 0

mpieva/quicksand

A pipeline for the analysis of sedimentary ancient mtDNA

Language: Nextflow - Size: 132 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 2

netreconlab/hipaa-postgres

HIPAA & GDPR compliant ready Postgres Database with PostGIS and PGAuditor

Language: Shell - Size: 200 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 2

singularityhub/docker2singularity

A docker image for converting docker images to singularity images.

Language: Shell - Size: 302 KB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 292 - Forks: 34

UPHL-BioNGS/Grandeur

UPHL's Reference Free Pipeline

Language: Nextflow - Size: 512 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 26 - Forks: 6

netreconlab/parse-hipaa-dashboard

Parse Dashboard for parse-hipaa server

Language: JavaScript - Size: 2.22 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 0

ucla-oarc-hpc/hpc_containers

Collection of Dockerfiles and Apptainer files used to create containers on Hoffman2

Language: Roff - Size: 101 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

PawseySC/hpc-container-training

Training material on using containers in an HPC setting.

Language: Python - Size: 110 MB - Last synced at: about 1 month ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 2

OpenOmics/mpox-seek

A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing

Language: Python - Size: 712 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

wilsontom/slurmwiz

Convert Mass Spectrometry Files using msconvert, singularity and SLURM

Language: R - Size: 12.7 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

Rick-van-Dam/Singularity 📦

A extremely fast ioc container for high performance applications

Language: C# - Size: 16.3 MB - Last synced at: 3 days ago - Pushed at: almost 5 years ago - Stars: 76 - Forks: 12

mkkoshkina/wf_denovo_sequencing

This is a Snakemake pipeline for de novo sequencing and annotation of MS peptidomics data

Language: Python - Size: 24.4 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

ENCCS/upscalingAIworkflows

Lesson material for Upscaling AI workflows

Language: Jupyter Notebook - Size: 11.2 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 2

ENCCS/containers 📦

Containers Lessons

Language: Python - Size: 3 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1

mbhall88/container_recipes

Repository with all my container recipes 👩‍🍳

Language: Dockerfile - Size: 99.6 KB - Last synced at: 7 days ago - Pushed at: 10 months ago - Stars: 16 - Forks: 6

unlhcc/singularity-dockerfiles

Read-only mirror of the HCC singularity dockerfiles repo.

Language: C++ - Size: 30.1 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 7 - Forks: 6

CCBR/Dockers

A collection of Dockerfiles to facilitate reproducibility across computing environments.

Language: Dockerfile - Size: 934 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 11 - Forks: 3

pscedu/singularity-octave

GNU Octave is software featuring a high-level programming language, primarily intended for numerical computations

Language: Shell - Size: 125 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 1

connectomicslab/connectomemapper3

Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.

Language: HTML - Size: 354 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 73 - Forks: 28