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Search results for pipeline snakemake
pipeline
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snakemake
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45 search results found
Sunbeam
⭐
157
A robust, extensible metagenomics pipeline
Dna Seq Gatk Variant Calling
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138
This Snakemake pipeline implements the GATK best-practices workflow
Sequana
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136
Sequana: a set of Snakemake NGS pipelines
Dropseqpipe
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134
A SingleCell RNASeq pre-processing snakemake workflow
Seq2science
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132
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
Tibanna
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68
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
Pyflow Chipseq
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55
a snakemake pipeline to process ChIP-seq files from GEO or in-house
Pytest Workflow
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52
Configure workflow/pipeline tests using yaml files.
Pipelines.jl
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39
A lightweight and powerful Julia package for computational pipelines and workflows.
Pyflow Atacseq
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37
ATAC-seq snakemake pipeline
Ngs_pipeline
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31
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Sopa
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25
Technology-invariant pipeline for spatial-omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
Atacseq_pipeline
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25
Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using bash and Python.
Mapache
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23
mapping pipeline for ancient DNA
Phylociraptor
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23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
Rna Seq Snakemake
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20
Snakemake based pipeline for RNA-Seq analysis
Varca
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20
Use an ensemble of variant callers to call variants from ATAC-seq data
Quaich
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19
snakemake pipeline for Hi-C post-processing
Pigx_rnaseq
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19
Pipeline for RNAseq
Mosaicatcher Pipeline
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19
Integrated workflow for SV calling from single-cell Strand-seq data
Kgwasflow
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19
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
Metameta
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18
Tailseeker
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18
Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer
Pigx
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15
Pipelines in genomics
Nbpipeline
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14
Snakemake-like pipeline manager for reproducible Jupyter Notebooks
Qadabra
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13
Snakemake workflow for comparison of differential abundance ranks
Ymp
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13
Flexible omics pipeline
Ngs Pipeline
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12
Pipeline for Somatic Variant Calling with WES and WGS data
Genome Seek
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12
Clinical Whole Genome Sequencing Pipeline
Catd_snakemake
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11
Snakemake pipeline for benchmarking cell-type deconvolution methods as well as deconvoluting real bulk RNA-seq data with the use of scRNA-seq datasets
Assnake
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10
Snakemake based framework for NGS data analysis and management
Proatac
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10
Preprocessing pipeline for (sc)ATAC data
Pigx_bsseq
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10
bisulfite sequencing pipeline from fastq to methylation reports
Cascabel
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10
Automated pipeline for amplicon sequence analysis
Monsda
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10
MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis
Enrichment_analysis
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10
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, and GSEApy.
Project Diploid Assembly
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8
Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data
Snakemake_rnaseq
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8
A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)
Zamp
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7
zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
Rnaseq_workflow
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6
snakemake workflow for bulk RNA-seq workflow using STAR-edgeR
Serpent Methylation Pipeline
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5
An efficient, documented, reproducible Snakemake methylation analysis pipeline for BS-seq and EM-seq samples, including cfDNA.
Xebec
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5
Snakemake pipeline for microbiome diversity effect size benchmarking
Celseq2
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5
Generate the UMI count matrix from CEL-Seq2 sequencing data
Allmine
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5
AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :
Bioinformatics_pipeline
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5
Bioinformatics Pipeline
As_analysis
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5
A complete Snakemake pipeline for detecting allele specific expression
Metagenomics
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5
Snakemake workflow for functional analysis of metagenomic WGS read data.
Genome_tracks
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5
A Snakemake workflow for easy visualization of genome browser tracks of aligned BAM files powered by the wrapper gtracks for the package pyGenomeTracks.
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