Repositories list

• Cirro-pipelines

  Public
  Pipeline configurations for cirro

  Python

  •

  MIT License

  •88 forks in CirroBio/Cirro-pipelines•00 stars in CirroBio/Cirro-pipelines•00 issues in CirroBio/Cirro-pipelines•22 pull requests in CirroBio/Cirro-pipelines•Updated Oct 23, 2026Oct 23, 2026

• spatial-data-studio

  Public
  Viewer for spatial transcriptomics analysis using the squidpy library

  TypeScript

  •

  Other

  •00 forks in CirroBio/spatial-data-studio•00 stars in CirroBio/spatial-data-studio•00 issues in CirroBio/spatial-data-studio•00 pull requests in CirroBio/spatial-data-studio•Updated Oct 22, 2026Oct 22, 2026

• wf-human-variation

  Public
  Nextflow

  •

  Other

  •8787 forks in CirroBio/wf-human-variation•00 stars in CirroBio/wf-human-variation•00 issues in CirroBio/wf-human-variation•00 pull requests in CirroBio/wf-human-variation•Updated Oct 22, 2026Oct 22, 2026

• wf-somatic-variation

  Public
  Nextflow

  •

  Other

  •1313 forks in CirroBio/wf-somatic-variation•00 stars in CirroBio/wf-somatic-variation•00 issues in CirroBio/wf-somatic-variation•00 pull requests in CirroBio/wf-somatic-variation•Updated Oct 22, 2026Oct 22, 2026

• Cirro-client-ts

  Public
  API client for TypeScript

  TypeScript

  •00 forks in CirroBio/Cirro-client-ts•00 stars in CirroBio/Cirro-client-ts•00 issues in CirroBio/Cirro-client-ts•00 pull requests in CirroBio/Cirro-client-ts•Updated Oct 22, 2026Oct 22, 2026

• Cirro-SDK-Python

  Public
  Python SDK to interact with Cirro

  Python

  •

  MIT License

  •33 forks in CirroBio/Cirro-SDK-Python•33 stars in CirroBio/Cirro-SDK-Python•44 issues in CirroBio/Cirro-SDK-Python•22 pull requests in CirroBio/Cirro-SDK-Python•Updated Oct 22, 2026Oct 22, 2026

• Cirro-client-python

  Public
  API client for Python

  Python

  •00 forks in CirroBio/Cirro-client-python•00 stars in CirroBio/Cirro-client-python•00 issues in CirroBio/Cirro-client-python•00 pull requests in CirroBio/Cirro-client-python•Updated Oct 22, 2026Oct 22, 2026

• Cirro-app-kit

  Public
  Developer guide, templates, scanner and Claude skills for standalone browser apps that sign in with Cirro

  TypeScript

  •00 forks in CirroBio/Cirro-app-kit•00 stars in CirroBio/Cirro-app-kit•00 issues in CirroBio/Cirro-app-kit•00 pull requests in CirroBio/Cirro-app-kit•Updated Oct 21, 2026Oct 21, 2026

• nf-cellranger-tools

  Public
  Collection of Nextflow tools for using CellRanger

  Nextflow

  •

  MIT License

  •22 forks in CirroBio/nf-cellranger-tools•00 stars in CirroBio/nf-cellranger-tools•00 issues in CirroBio/nf-cellranger-tools•00 pull requests in CirroBio/nf-cellranger-tools•Updated Oct 20, 2026Oct 20, 2026

• Cirro-install-resources

  Public
  Repository for CloudFormation templates used to install Cirro

  HCL

  •11 fork in CirroBio/Cirro-install-resources•11 star in CirroBio/Cirro-install-resources•00 issues in CirroBio/Cirro-install-resources•11 pull request in CirroBio/Cirro-install-resources•Updated Oct 16, 2026Oct 16, 2026

• nf-flowjo-gating

  Public
  Apply gates from a FlowJo workspace to a new set of FCS files

  R

  •00 forks in CirroBio/nf-flowjo-gating•00 stars in CirroBio/nf-flowjo-gating•00 issues in CirroBio/nf-flowjo-gating•00 pull requests in CirroBio/nf-flowjo-gating•Updated Oct 13, 2026Oct 13, 2026

• terraform-provider-cirro

  Public
  Terraform provider for managing your Cirro tenant

  Go

  •00 forks in CirroBio/terraform-provider-cirro•00 stars in CirroBio/terraform-provider-cirro•00 issues in CirroBio/terraform-provider-cirro•00 pull requests in CirroBio/terraform-provider-cirro•Updated Oct 7, 2026Oct 7, 2026

• img2tiff

  Public
  Conveneince methods to convert various image formats to OME Tiff with QuPath

  Nextflow

  •

  MIT License

  •22 forks in CirroBio/img2tiff•00 stars in CirroBio/img2tiff•00 issues in CirroBio/img2tiff•00 pull requests in CirroBio/img2tiff•Updated Oct 6, 2026Oct 6, 2026

• nf-differential-expression

  Public
  Workflow for performing differential expression analysis from gene abundance data

  Python

  •22 forks in CirroBio/nf-differential-expression•00 stars in CirroBio/nf-differential-expression•00 issues in CirroBio/nf-differential-expression•00 pull requests in CirroBio/nf-differential-expression•Updated Sep 25, 2026Sep 25, 2026

• nf-arcashla

  Public
  Nextflow workflow to perform HLA typing from RNAseq data (arcasHLA)

  Nextflow

  •11 fork in CirroBio/nf-arcashla•11 star in CirroBio/nf-arcashla•00 issues in CirroBio/nf-arcashla•00 pull requests in CirroBio/nf-arcashla•Updated Sep 24, 2026Sep 24, 2026

• Cirro-local-agent

  Public
  Agent to run workloads on local HPC environment

  Java

  •

  MIT License

  •00 forks in CirroBio/Cirro-local-agent•11 star in CirroBio/Cirro-local-agent•00 issues in CirroBio/Cirro-local-agent•00 pull requests in CirroBio/Cirro-local-agent•Updated Sep 21, 2026Sep 21, 2026

• nf-exec

  Public
  Execute arbitrary command using Nextflow

  Nextflow

  •00 forks in CirroBio/nf-exec•00 stars in CirroBio/nf-exec•11 issue in CirroBio/nf-exec•00 pull requests in CirroBio/nf-exec•Updated Sep 17, 2026Sep 17, 2026

• amazon-ebs-autoscale

  Public
  Don't run out of disk space on your EC2 instance when generating or working with large files. Automatically add EBS volumes to a filesystem mount point in respo…

  Shell

  •

  MIT License

  •6262 forks in CirroBio/amazon-ebs-autoscale•00 stars in CirroBio/amazon-ebs-autoscale•00 issues in CirroBio/amazon-ebs-autoscale•00 pull requests in CirroBio/amazon-ebs-autoscale•Updated Sep 8, 2026Sep 8, 2026

• Cirro-jbrowse-config

  Public
  Utilities to generate genome browser visualizations using JBrowse

  Python

  •00 forks in CirroBio/Cirro-jbrowse-config•00 stars in CirroBio/Cirro-jbrowse-config•00 issues in CirroBio/Cirro-jbrowse-config•00 pull requests in CirroBio/Cirro-jbrowse-config•Updated Sep 8, 2026Sep 8, 2026

• nf-cell-segment

  Public
  Identify cells from high resolution images

  Python

  •

  MIT License

  •00 forks in CirroBio/nf-cell-segment•11 star in CirroBio/nf-cell-segment•00 issues in CirroBio/nf-cell-segment•00 pull requests in CirroBio/nf-cell-segment•Updated Aug 21, 2026Aug 21, 2026

• Cirro-data-transfer-utility

  Public
  Interactive tool to manage the transfer of data into Cirro

  Python

  •00 forks in CirroBio/Cirro-data-transfer-utility•00 stars in CirroBio/Cirro-data-transfer-utility•00 issues in CirroBio/Cirro-data-transfer-utility•00 pull requests in CirroBio/Cirro-data-transfer-utility•Updated Aug 14, 2026Aug 14, 2026

• nf-index-genome

  Public
  Utilities for building genome indices

  Nextflow

  •00 forks in CirroBio/nf-index-genome•00 stars in CirroBio/nf-index-genome•00 issues in CirroBio/nf-index-genome•00 pull requests in CirroBio/nf-index-genome•Updated Jul 9, 2026Jul 9, 2026

• nf-core-onboarding

  Public
  Cirro pipeline configurations for onboarding nf-core pipelines into the development account (not production). Layout: nf-core/<pipeline>/<version>/.

  Python

  •00 forks in CirroBio/nf-core-onboarding•00 stars in CirroBio/nf-core-onboarding•00 issues in CirroBio/nf-core-onboarding•00 pull requests in CirroBio/nf-core-onboarding•Updated Jun 15, 2026Jun 15, 2026

• nf-convert-seurat-to-h5ad

  Public
  Nextflow workflow to convert Seurat objects (.rds) to cellxgene-compatible AnnData (.h5ad)

  Nextflow

  •00 forks in CirroBio/nf-convert-seurat-to-h5ad•00 stars in CirroBio/nf-convert-seurat-to-h5ad•00 issues in CirroBio/nf-convert-seurat-to-h5ad•00 pull requests in CirroBio/nf-convert-seurat-to-h5ad•Updated Feb 6, 2026Feb 6, 2026

• biomcp

  Public
  BioMCP: Biomedical Model Context Protocol

  Python

  •

  MIT License

  •120120 forks in CirroBio/biomcp•00 stars in CirroBio/biomcp•00 issues in CirroBio/biomcp•00 pull requests in CirroBio/biomcp•Updated Jan 14, 2026Jan 14, 2026

• nf-azimuth

  Public
  Nextflow workflow running Azimuth

  Python

  •00 forks in CirroBio/nf-azimuth•00 stars in CirroBio/nf-azimuth•00 issues in CirroBio/nf-azimuth•00 pull requests in CirroBio/nf-azimuth•Updated Sep 16, 2025Sep 16, 2025

• nf-gene-set-enrichment

  Public
  Nextflow

  •11 fork in CirroBio/nf-gene-set-enrichment•00 stars in CirroBio/nf-gene-set-enrichment•00 issues in CirroBio/nf-gene-set-enrichment•00 pull requests in CirroBio/nf-gene-set-enrichment•Updated Sep 11, 2025Sep 11, 2025

• nf-sourmash

  Public
  Nextflow workflow running sourmash

  Nextflow

  •11 fork in CirroBio/nf-sourmash•00 stars in CirroBio/nf-sourmash•00 issues in CirroBio/nf-sourmash•00 pull requests in CirroBio/nf-sourmash•Updated Jul 3, 2025Jul 3, 2025

• nf-xenium-ranger

  Public
  Nextflow workflow running Xenium Ranger

  Nextflow

  •00 forks in CirroBio/nf-xenium-ranger•00 stars in CirroBio/nf-xenium-ranger•00 issues in CirroBio/nf-xenium-ranger•00 pull requests in CirroBio/nf-xenium-ranger•Updated Jan 13, 2025Jan 13, 2025

• Tool-rawgraphs-app

  Public
  A web interface to create custom vector-based visualizations on top of RAWGraphs core

  JavaScript

  •

  Apache License 2.0

  •1.8k1.8k forks in CirroBio/Tool-rawgraphs-app•00 stars in CirroBio/Tool-rawgraphs-app•00 issues in CirroBio/Tool-rawgraphs-app•00 pull requests in CirroBio/Tool-rawgraphs-app•Updated Jan 5, 2025Jan 5, 2025