OpenOmics/chrom-seek

An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq

Language: Python - Size: 1.24 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 5 - Forks: 3

OpenOmics/space-seek

Spatial-sequencing: The final frontier. These are the voyages of the 10x Visium pipeline, space-seek.

Language: Python - Size: 573 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 1 - Forks: 0

OpenOmics/metamorph

Metagenomics and Metatranscriptomics pipeline

Language: Python - Size: 8.75 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 5 - Forks: 2

OpenOmics/Markowitz_HPV_CCC_analysis

Size: 1.95 KB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 0 - Forks: 0

OpenOmics/microscope

A shiny-based all-in-one microbiome diversity and taxonomy viewer

Language: R - Size: 5.25 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

OpenOmics/genome-seek

Clinical Whole Genome and Exome Sequencing Pipeline

Language: Python - Size: 952 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 23 - Forks: 10

OpenOmics/cell-seek

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.

Language: Python - Size: 737 KB - Last synced at: 3 days ago - Pushed at: 16 days ago - Stars: 1 - Forks: 1

OpenOmics/RNA-seek Fork of skchronicles/RNA-seek

A comprehensive quality-control and quantification RNA-seq pipeline

Language: Python - Size: 10.3 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 2

OpenOmics/scribble

Scripts/code-snippets, somewhere in-between bioinformatics and data science, and oneliners

Language: Python - Size: 552 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 3

OpenOmics/methyl-seek

Bisulphite-sequencing DNA methylation pipeline

Language: Python - Size: 655 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 7 - Forks: 3

OpenOmics/leafworker

An awesome snakemake pipeline to run leafcutter.

Language: Python - Size: 688 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

OpenOmics/mpox-seek

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

Language: Python - Size: 712 KB - Last synced at: 3 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

OpenOmics/NIDDK-15

Language: R - Size: 83 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

OpenOmics/mir-seek

An awesome microRNA-sequencing pipeline

Language: Python - Size: 595 KB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 2 - Forks: 1

OpenOmics/NHLBI-186

Human bulk RNA seq analysis

Language: R - Size: 98.6 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1

OpenOmics/nanite

A streamlined Oxford Nanopore Viral Metagenomics Pipeline

Language: Python - Size: 627 KB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 4 - Forks: 2

OpenOmics/mr-seek

Mendelian Randomization pipeline

Language: Python - Size: 749 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 1

OpenOmics/snakevision

An awesome tool to visualize snakemake rule graphs

Language: Python - Size: 43 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 8 - Forks: 0

OpenOmics/baseline

A BASE template for building pipeLINEs

Language: Python - Size: 541 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 1

OpenOmics/scErvx

Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with data from 10x genomics (bam files)

Language: Python - Size: 598 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

OpenOmics/pbAmp-seek

Identify and count PacBio Hifi amplicons

Language: Python - Size: 538 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 2

OpenOmics/parabricks-benchmark

Benchmarking parabricks GPU-accelerated tools for GATK and beyond!

Language: Python - Size: 547 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

OpenOmics/modr

An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

Language: Python - Size: 689 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 5 - Forks: 1

OpenOmics/metavirs

Viral Metagenomics Assembly and Annotation Pipeline

Language: Python - Size: 695 KB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 5 - Forks: 1

OpenOmics/istari

Perform error-prone data preparation for whole genome regression modeling

Language: Python - Size: 745 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

OpenOmics/cyte-seek

Awesome single-cell CITE-sequencing Pipeline

Language: Python - Size: 708 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

OpenOmics/HiIP

An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.

Language: Python - Size: 577 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

OpenOmics/assembly-seek

De novo Long-read Genome Assembly Pipeline

Language: Python - Size: 577 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 2

OpenOmics/ervx

Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with bulk RNA

Language: Python - Size: 908 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 1

OpenOmics/dockerfiles

Dockerfiles for reproducible scientific research and beyond!

Language: Python - Size: 176 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1

OpenOmics/weave

An awesome BCL demultiplexing and FastQ quality-control pipeline

Language: Python - Size: 1.5 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

OpenOmics/SnakeMaker Fork of tomh1lll/FunannotateMake

A repository for the Maker Snakemake pipeline

Language: Python - Size: 118 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 1

OpenOmics/profiles

A universal set of snakemake profiles for different clusters at the NIH

Language: Python - Size: 55.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

OpenOmics/SnakeMaker_alt Fork of OpenOmics/SnakeMaker

A repository for the Maker Snakemake pipeline

Language: Python - Size: 127 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

OpenOmics/brakerMake

Snakemake pipeline for annotating with braker and adding functional information

Language: Python - Size: 558 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

OpenOmics/NCBR-492

Metagenome analysis for bacterial pure colonies

Language: Shell - Size: 21.4 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 1

OpenOmics/project-template

An awesome, minimal github template for your projects

Language: R - Size: 10.7 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

OpenOmics/drep Fork of MrOlm/drep

Rapid comparison and dereplication of genomes

Language: Python - Size: 16.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

OpenOmics/chromoscope Fork of hms-dbmi/chromoscope

Interactive multiscale visualization for structural variation in human genomes

Language: TypeScript - Size: 308 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

OpenOmics/cfChIP-seek 📦

cell-free ChIP-seq pipeline

Language: Python - Size: 758 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 3

OpenOmics/GRS_SC10X

A pipeline for 10X cellranger

Language: Python - Size: 34.2 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

OpenOmics/MRPlotly

R package for performing Mendelian randomization with GWAS summary data

Language: R - Size: 41 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0

OpenOmics/DeepSeq

Ultra Deep Amplicon Sequencing Analysis of NPM1 gene

Language: Python - Size: 54.7 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

OpenOmics/nih-box

Archive, share, and explore projects and files on Box@NIH

Language: Python - Size: 486 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

OpenOmics/ATAC-seq Fork of NCBR-FNLCR/ATAC-seq

Language: Python - Size: 79.1 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1

OpenOmics/DLscID

Deep Learning single-cell Identification and Annotation

Language: Python - Size: 480 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

OpenOmics/.github

OpenOmics organizational profile

Size: 584 KB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

OpenOmics/SQANTImake Fork of tomh1lll/SQANTImake

Pipeline to generate custom SQANTI GTF & modify it for use in RNA-seek

Size: 40 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

OpenOmics/HERVx Fork of CCBR/HERVx

Pipeline to characterize Human Endogenous Retrovirus (HERV) expression

Language: Shell - Size: 5.75 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

OpenOmics/Long-read-genome-assembly Fork of NCBR-FNLCR/Long-read-genome-assembly

PacBio data

Size: 16.6 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

OpenOmics/viral_variant_pipeline Fork of niaid/viral_variant_pipeline

BCBB minion viral assembly pipeline

Size: 65.4 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0