OpenOmics

All

43 repositories

scribble
Public
Scripts/code-snippets, somewhere in-between bioinformatics and data science, and oneliners
Python
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MIT License
•3•4•0•0•Updated Nov 7, 2024Nov 7, 2024
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
•
MIT License
•2•5•10•0•Updated Nov 6, 2024Nov 6, 2024
metamorph
Public
Metagenomics and Metatranscriptomics pipeline
quality-control snakemake pipeline metagenomics metatranscriptomics
Python
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MIT License
•1•5•3•0•Updated Nov 6, 2024Nov 6, 2024
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
•11•18•4•0•Updated Nov 5, 2024Nov 5, 2024
mir-seek
Public
An awesome microRNA-sequencing pipeline
snakemake singularity mirna mirdeep2 mirna-seq micro-rna micro-rna-expression mature-mirna
Python
•
MIT License
•1•1•1•0•Updated Oct 1, 2024Oct 1, 2024
mutation-seek
Public
An awesome quantitative genetics pipeline
Python
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MIT License
•0•0•0•0•Updated Sep 19, 2024Sep 19, 2024
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•1•0•0•Updated Sep 17, 2024Sep 17, 2024
mpox-seek
Public
A rapid pipeline for targeted ONT monkeypox sequencing
snakemake pipeline conda rapid singularity phylogenetics oxford-nanopore mamba monkeypox mpox
Python
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MIT License
•0•1•0•0•Updated Aug 22, 2024Aug 22, 2024
dockerfiles
Public
Dockerfiles for reproducible scientific research and beyond!
Python
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MIT License
•1•0•0•0•Updated Aug 19, 2024Aug 19, 2024
project-template
Public template
An awesome, minimal github template for your projects
project-template
R
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MIT License
•1•1•0•0•Updated Aug 15, 2024Aug 15, 2024
brakerMake
Public
Snakemake pipeline for annotating with braker and adding functional information
Python
•0•1•0•0•Updated Aug 15, 2024Aug 15, 2024
methyl-seek
Public
Bisulphite-sequencing based methylation pipeline
Python
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MIT License
•3•6•0•1•Updated Aug 13, 2024Aug 13, 2024
drep
Public
Rapid comparison and dereplication of genomes
Python
•37•0•0•0•Updated Aug 12, 2024Aug 12, 2024
parabricks-benchmark
Public
Benchmarking parabricks GPU-accelerated tools for GATK and beyond!
Python
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MIT License
•0•1•0•0•Updated Jul 11, 2024Jul 11, 2024
baseline
Public template
A BASE template for building pipeLINEs
snakemake pipeline-template
Python
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MIT License
•1•3•1•0•Updated Jun 24, 2024Jun 24, 2024
ervx
Public
Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with bulk RNA
workflow quality-control snakemake pipeline human mouse singularity herv endogenous-retrovirus-expression
Python
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MIT License
•1•1•1•0•Updated Jun 20, 2024Jun 20, 2024
nanite
Public
A streamlined Oxford Nanopore Viral Metagenomics Pipeline
snakemake annotation assembly slim singularity classification viral-metagenomics pathogen-surveillance pipeline
Python
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MIT License
•2•4•0•0•Updated Jun 6, 2024Jun 6, 2024
RNA-seek
Public
A comprehensive quality-control and quantification RNA-seq pipeline
Python
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MIT License
•12•4•0•1•Updated Mar 30, 2024Mar 30, 2024
HiIP
Public
An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.
snakemake pipeline singularity hi-c chip-seq hichip
Python
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MIT License
•0•0•1•0•Updated Mar 19, 2024Mar 19, 2024
assembly-seek
Public
De novo Long-read Genome Assembly Pipeline
Python
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MIT License
•2•2•4•0•Updated Mar 15, 2024Mar 15, 2024
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•5•0•Updated Feb 28, 2024Feb 28, 2024
chromoscope
Public
Interactive multiscale visualization for structural variation in human genomes
TypeScript
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MIT License
•6•1•0•0•Updated Feb 15, 2024Feb 15, 2024
profiles
Public
A universal set of snakemake profiles for different clusters at the NIH
Python
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MIT License
•0•1•0•0•Updated Feb 8, 2024Feb 8, 2024
cfChIP-seek
Public archive
cell-free ChIP-seq pipeline
quality-control snakemake chip-seq cell-free-dna peak-calling peak-annotation cell-type-deconvolution
Python
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MIT License
•3•3•0•0•Updated Feb 7, 2024Feb 7, 2024
modr
Public
An awesome Oxford Nanopore Pipeline for direct RNA-sequencing
bioinformatics quality-control pipeline singularity alternative-splicing-analysis transcriptomics oxford-nanopore rna-editing differential-expression-analysis snakemake-pipeline
Python
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MIT License
•1•5•2•0•Updated Feb 6, 2024Feb 6, 2024
metavirs
Public
Viral Metagenomics Assembly and Annotation Pipeline
quality-control snakemake annotation assembly singularity classification viral-metagenomics pathogen-surveillance pipeline
Python
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MIT License
•1•4•2•0•Updated Feb 6, 2024Feb 6, 2024
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•2•1•0•Updated Nov 30, 2023Nov 30, 2023
cyte-seek
Public
Awesome single-cell CITE-sequencing Pipeline
quality-control singularity single-cell 10xgenomics cite-seq pipeline
Python
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MIT License
•0•2•0•0•Updated Sep 12, 2023Sep 12, 2023
scErvx
Public
Endogenous Retrovirus Expression Pipeline for Human and Mouse for use with data from 10x genomics (bam files)
single-cell-rna-seq endogenous-retrovirus-expression
Python
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MIT License
•0•1•0•0•Updated Sep 12, 2023Sep 12, 2023
GRS_SC10X
Public
A pipeline for 10X cellranger
Python
•0•0•0•0•Updated Aug 22, 2023Aug 22, 2023