OpenOmics

Open Bioinformatics Research

United States of America

Pinned Repositories

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:Python1 1 01
chrom-seek
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
Language:Python5 5 292
genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
Language:Python18 1 1811
metamorph
Metagenomics and Metatranscriptomics pipeline
Language:Python5 2 131
metavirs
Viral Metagenomics Assembly and Annotation Pipeline
Language:Python4 2 141
methyl-seek
Bisulphite-sequencing based methylation pipeline
Language:Python6 2 03
modr
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
Language:Python5 1 21
MRPlotly
R package for performing Mendelian randomization with GWAS summary data
Language:R5 1 00
RNA-seek
A comprehensive quality-control and quantification RNA-seq pipeline
Language:Python4 0 02
scribble
Scripts/code-snippets, somewhere in-between bioinformatics and data science, and oneliners
Language:Python4 9 03

OpenOmics's Repositories

OpenOmics/genome-seek
Clinical Whole Genome and Exome Sequencing Pipeline
Language:Python18 1 1811
OpenOmics/methyl-seek
Bisulphite-sequencing based methylation pipeline
Language:Python6 2 03
OpenOmics/chrom-seek
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
Language:Python5 5 292
OpenOmics/metamorph
Metagenomics and Metatranscriptomics pipeline
Language:Python5 2 131
OpenOmics/modr
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
Language:Python5 1 21
OpenOmics/metavirs
Viral Metagenomics Assembly and Annotation Pipeline
Language:Python4 2 141
OpenOmics/nanite
A streamlined Oxford Nanopore Viral Metagenomics Pipeline
Language:Python4 1 02
OpenOmics/RNA-seek
A comprehensive quality-control and quantification RNA-seq pipeline
Language:Python4 0 02
OpenOmics/scribble
Scripts/code-snippets, somewhere in-between bioinformatics and data science, and oneliners
Language:Python4 9 03
OpenOmics/baseline
A BASE template for building pipeLINEs
Language:Python3 1 31
OpenOmics/cfChIP-seek
cell-free ChIP-seq pipeline
Language:Python3 1 03
OpenOmics/snakevision
An awesome tool to visualize snakemake rule graphs
Language:Python3 1 1
OpenOmics/assembly-seek
De novo Long-read Genome Assembly Pipeline
Language:Python2 2 92
OpenOmics/cyte-seek
Awesome single-cell CITE-sequencing Pipeline
Language:Python2 1 10
OpenOmics/brakerMake
Snakemake pipeline for annotating with braker and adding functional information
Language:Python1 1 0
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:Python1 1 01
OpenOmics/chromoscope
Interactive multiscale visualization for structural variation in human genomes
Language:TypeScript1 0 0
OpenOmics/ervx
Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with bulk RNA
Language:Python1 2 11
OpenOmics/mir-seek
An awesome microRNA-sequencing pipeline
Language:Python1 1 21
OpenOmics/mpox-seek
A rapid pipeline for targeted ONT monkeypox sequencing
Language:Python1 1 0
OpenOmics/parabricks-benchmark
Benchmarking parabricks GPU-accelerated tools for GATK and beyond!
Language:Python1 1 0
OpenOmics/profiles
A universal set of snakemake profiles for different clusters at the NIH
Language:Python1 2 0
OpenOmics/project-template
An awesome, minimal github template for your projects
Language:R1 1 01
OpenOmics/scErvx
Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with data from 10x genomics (bam files)
Language:Python1 2 0
OpenOmics/weave
An awesome BCL demultiplexing and FastQ quality-control pipeline
Language:Python1 2 180
OpenOmics/dockerfiles
Dockerfiles for reproducible scientific research and beyond!
Language:Python1 01
OpenOmics/drep
Rapid comparison and dereplication of genomes
Language:Python
OpenOmics/HiIP
An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.
Language:Python1 1
OpenOmics/mutation-seek
An awesome quantitative genetics pipeline
Language:Python
OpenOmics/NCBR-492
Metagenome analysis for bacterial pure colonies
Language:Shell1