OpenOmics

All

61 repositories

cell-seek
Public
One single-cell pipeline to rule them all, one pipeline to find them, one pipeline to unify them all, and with the data bind them.
10xgenomics single-cell-rna-seq single-cell-atac-seq single-cell-omics single-cell-vdj single-cell-cite-seq
Python
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MIT License
•1•2•5•1•Updated Feb 23, 2026Feb 23, 2026
leafworker
Public
An awesome alternative-splicing pipeline that runs leafcutter and IsoformSwitchAnalyzeR.
alternative-splicing differential-analysis isoform-quantification isoform-switches covariate-correction
Python
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MIT License
•0•1•3•0•Updated Feb 17, 2026Feb 17, 2026
ShinyCell2
Public
ShinyCell2 is a lightweight R package for building interactive, shareable apps to explore single-cell multi-omics, scATAC-seq and spatial transcriptomics data w…
R
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GNU General Public License v3.0
•12•0•0•0•Updated Feb 13, 2026Feb 13, 2026
scribble
Public
Scripts/code-snippets, somewhere in-between bioinformatics and data science, and oneliners
Python
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MIT License
•4•4•0•0•Updated Feb 13, 2026Feb 13, 2026
chrom-seek
Public
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
quality-control annotation chip-seq atac-seq bulk cell-free-dna peak-calling differential-accessibility differential-binding
Python
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MIT License
•3•5•7•0•Updated Feb 13, 2026Feb 13, 2026
shiny-forge
Public
A tool to deploy shinycell applications to infinity and beyond (dockerhub and GCP)!
Python
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MIT License
•0•0•3•0•Updated Feb 5, 2026Feb 5, 2026
.github
Public
OpenOmics Organization Profile
1•0•0•0•Updated Feb 3, 2026Feb 3, 2026
openomics.github.io
Public
OpenOmics home page
Python
•0•0•3•0•Updated Feb 3, 2026Feb 3, 2026
NCBR-533
Public
Identifying antibiotic resistance genes in all publicly available Staphylococcus aureus genomic and plasmid sequences
Python
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MIT License
•0•0•0•0•Updated Jan 29, 2026Jan 29, 2026
RNA-seek
Public
A comprehensive quality-control and quantification RNA-seq pipeline
quality-control rna-seq gene-expression differential-expression-analysis gene-fusions isoform-expression
Python
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MIT License
•13•5•0•0•Updated Jan 21, 2026Jan 21, 2026
arc
Public
An awesome tool to archive projects
Python
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MIT License
•0•0•2•0•Updated Jan 21, 2026Jan 21, 2026
iso-seek
Public
An awesome pipeline for processing bulk PacBio transcriptomics data generated with ISO-seq and MAS-seq.
snakemake singularity iso-seq long-read-sequencing pacbio-sequencing mas-seq
Python
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MIT License
•0•0•0•0•Updated Jan 16, 2026Jan 16, 2026
snakevision
Public
An awesome tool to visualize snakemake rule graphs
visualization snakemake networkx dag dot-graphics rulegraph dagviz
Python
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MIT License
•0•15•1•0•Updated Jan 9, 2026Jan 9, 2026
fragmentomics
Public
A pipeline analyzing fragmentomics profile of cfDNA sequencing data
cell-free-dna fragmentomics cfdna-profiling fragment-features
Python
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MIT License
•0•0•1•0•Updated Dec 19, 2025Dec 19, 2025
NHLBI-1084
Public
NHLBI-1084
Python
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MIT License
•0•0•0•0•Updated Dec 16, 2025Dec 16, 2025
dockerfiles
Public
Dockerfiles for reproducible scientific research and beyond!
Python
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MIT License
•1•0•0•0•Updated Dec 15, 2025Dec 15, 2025
mir-seek
Public
An awesome microRNA-sequencing pipeline
snakemake singularity mirna mirdeep2 mirna-seq micro-rna micro-rna-expression mature-mirna
Python
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MIT License
•1•2•2•0•Updated Dec 15, 2025Dec 15, 2025
Markowitz_HPV_CCC_analysis
Public
R
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MIT License
•0•0•0•0•Updated Nov 20, 2025Nov 20, 2025
genome-seek
Public
Clinical Whole Genome and Exome Sequencing Pipeline
quality-control snakemake pipeline somatic-variants singularity copy-number-variation whole-exome-sequencing whole-genome-sequencing variant-annotation hla-typing
Python
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MIT License
•12•29•5•0•Updated Oct 27, 2025Oct 27, 2025
NIAID-1163
Public
Scripting for project NIAID-1163 and Microbiology Resource Announcements publication
Python
•0•0•0•0•Updated Oct 20, 2025Oct 20, 2025
upset2-report
Public
Builds a stand-alone, shareable Upset2 report from a set of files
Python
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MIT License
•0•1•0•0•Updated Oct 10, 2025Oct 10, 2025
methyl-seek
Public
Bisulphite-sequencing DNA methylation pipeline
deconvolution dmr cell-free-dna bisulfite-sequencing
Python
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MIT License
•3•7•2•1•Updated Sep 15, 2025Sep 15, 2025
metamorph
Public
Metagenomics and Metatranscriptomics pipeline
quality-control snakemake pipeline metagenomics metatranscriptomics
Python
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MIT License
•2•5•2•0•Updated Sep 12, 2025Sep 12, 2025
space-seek
Public
Spatial-sequencing: The final frontier. These are the voyages of the 10x Visium pipeline, space-seek.
snakemake pipeline singularity single-cell 10xgenomics visium-hd
Python
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MIT License
•0•1•0•0•Updated Sep 4, 2025Sep 4, 2025
microscope
Public
A shiny-based all-in-one microbiome diversity and taxonomy viewer
R
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MIT License
•1•0•0•0•Updated Aug 8, 2025Aug 8, 2025
shiny-somascan
Public
An R package and shiny application for somascan power analysis.
MIT License
•0•0•0•0•Updated Aug 1, 2025Aug 1, 2025
ervx
Public
Endogenous Retrovirus Expression Pipeline for Human, Mouse, and Macaque for use with bulk RNA-seq
workflow quality-control snakemake pipeline human mouse singularity herv transposable-elements endogenous-retrovirus-expression
Python
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MIT License
•1•1•2•0•Updated Jul 17, 2025Jul 17, 2025
mpox-seek
Public
A rapid pipeline for targeted and whole-genome ONT monkeypox sequencing
snakemake pipeline rapid singularity phylogenetics oxford-nanopore mamba viral-genomics monkeypox
Python
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MIT License
•0•1•0•0•Updated May 20, 2025May 20, 2025
weave
Public
An awesome BCL demultiplexing and FastQ quality-control pipeline
kaiju bcl2fastq fastp krona kraken2 bclconvert fastq-quality-control contamination-screening disambiguate-genomes
Python
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MIT License
•0•1•6•1•Updated Apr 22, 2025Apr 22, 2025
profiles
Public
A universal set of snakemake profiles for different clusters at the NIH
Python
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MIT License
•0•2•0•0•Updated Apr 15, 2025Apr 15, 2025