Topic: snakemake Goto Github
Some thing interesting about snakemake
Some thing interesting about snakemake
snakemake, 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.
Organization: 4dn-dcic
snakemake,Close assembly gaps using long-reads at high accuracy.
User: a-ludi
Home Page: https://a-ludi.github.io/dentist/
snakemake,kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
User: akcorut
Home Page: https://github.com/akcorut/kGWASflow/wiki
snakemake,Amplicon sequence processing workflow using QIIME 2 and Snakemake
Organization: aomlomics
snakemake,V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Organization: cbg-ethz
Home Page: https://cbg-ethz.github.io/V-pipe/
snakemake,A lightweight and powerful Julia package for computational pipelines and workflows.
User: cihga39871
snakemake,🦠📇 Microbial genomes-to-report pipeline
User: cmkobel
Home Page: https://CompareM2.readthedocs.io
snakemake,ATAC-seq snakemake pipeline
User: crazyhottommy
snakemake,a snakemake pipeline to process ChIP-seq files from GEO or in-house
User: crazyhottommy
snakemake,RNAseq analysis notes from Ming Tang
User: crazyhottommy
snakemake,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.
Organization: epigen
Home Page: https://epigen.github.io/atacseq_pipeline/
snakemake,:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
User: franciscozorrilla
Home Page: https://franciscozorrilla.github.io/metaGEM/
snakemake,Accompanying analysis code for the FRASER manuscript
Organization: gagneurlab
Home Page: https://tinyurl.com/FRASER-paper
snakemake,Snakemake-based workflow for detecting structural variants in genomic data
Organization: googlingthecancergenome
Home Page: https://research-software.nl/software/sv-callers
snakemake,Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
Organization: gustaveroussy
Home Page: https://gustaveroussy.github.io/sopa/
snakemake,A framework for keeping biomedical text mining result up-to-date
User: jakelever
snakemake,A simple Snakemake profile for Slurm without --cluster-config
User: jdblischak
snakemake,Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
Organization: jetbrains-research
snakemake,multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))
User: joybio
snakemake,[MIRROR] Emacs support for Snakemake
User: kyleam
Home Page: https://git.kyleam.com/snakemake-mode/about/
snakemake,reproducible research project template for R using Renv and snakemake with an econ application
User: lachlandeer
Home Page: https://lachlandeer.github.io/snakemake-econ-r-tutorial/
snakemake,Configure workflow/pipeline tests using yaml files.
Organization: lumc
Home Page: https://pytest-workflow.readthedocs.io/en/stable/
snakemake,Customizable workflows based on snakemake and python for the analysis of NGS data
Organization: maxplanck-ie
Home Page: http://snakepipes.readthedocs.io
snakemake,ATLAS - Three commands to start analyzing your metagenome data
Organization: metagenome-atlas
Home Page: https://metagenome-atlas.github.io/
snakemake,A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
Organization: moiexpositoalonsolab
Home Page: http://grene-net.org
snakemake,ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications
User: ncherric
Home Page: https://iliad.readthedocs.io/
snakemake,Monitor computational workflows in real time
Organization: panoptes-organization
snakemake,Explore the impacts of 24/7 Carbon-Free Energy PPAs
Organization: pypsa
snakemake,PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System
Organization: pypsa
Home Page: https://pypsa-eur.readthedocs.io/
snakemake,rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
User: reslp
Home Page: https://phylociraptor.readthedocs.io
snakemake,🔬🖥 Automated Blood Vasculature Analysis of 3D Light-Sheet Image Volumes
Organization: rub-bioinf
snakemake,Snakemake based pipeline for RNA-Seq analysis
User: saketkc
snakemake,:snake: Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).
User: slowkow
Home Page: https://slowkow.com/notes/snakemake-tutorial/
snakemake,Snakemake profile for running jobs on an LSF cluster
Organization: snakemake-profiles
snakemake,A cookiecutter template for Snakemake workflows
Organization: snakemake-workflows
snakemake,This Snakemake pipeline implements the GATK best-practices workflow
Organization: snakemake-workflows
snakemake,A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
Organization: snakemake-workflows
snakemake,Documentation of the Snakemake-Workflows project
Organization: snakemake-workflows
snakemake,A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
Organization: snakemake-workflows
snakemake,RNA-seq workflow using STAR and DESeq2
Organization: snakemake-workflows
snakemake,This is the development home of the workflow management system Snakemake. For general information, see
Organization: snakemake
Home Page: https://snakemake.github.io
snakemake,A robust, extensible metagenomics pipeline
Organization: sunbeam-labs
Home Page: http://sunbeam.readthedocs.io
snakemake,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.
Organization: vanheeringen-lab
Home Page: https://vanheeringen-lab.github.io/seq2science
snakemake,The Zavolab Automated RNA-seq Pipeline
Organization: zavolanlab
Home Page: https://zavolanlab.github.io/zarp/
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