cookiecutter-snakemake-workflow
RNA-seq-analysis
| cookiecutter-snakemake-workflow | RNA-seq-analysis | |
|---|---|---|
| 1 | 1 | |
| 55 | 840 | |
| - | - | |
| 1.8 | 0.0 | |
| over 2 years ago | over 2 years ago | |
| Python | Python | |
| MIT License | MIT License |
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For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
cookiecutter-snakemake-workflow
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Development notes in Snakemake workflows
I currently use cookiecutter to start new Snakemake repositories (projects) because it's really comfortable and guarantees that I follow an organized and recommended directory structure. However, I have a tendency to make notes during development. Maybe I made some decision based on something I learned in biostars or reddit and I want to remember that, or I start by outlining my workflow steps in written form. So far I've used both the README file and the Snakemake file (comments) to do that, but I'm wondering if anyone has a suggestion for how to fit development notes within a Snakemake project.
RNA-seq-analysis
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Looking for advice regarding R-programming and data analysis for immunology/biology projects
One github user crazyhottommy has repositories that cover multiple tools related to several sequencing experiments also including RNA-seq. Really good stuff https://github.com/crazyhottommy/RNA-seq-analysis
What are some alternatives?
cookiecutter-data-science - A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
COVID-19-RNA-Seq-datasets - A repository for sharing information on available COVID-19 RNA-Seq datasets
pypsa-eur - PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System
metaGEM - :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
zarp - The Zavolab Automated RNA-seq Pipeline
FastAPI-template - Feature rich robust FastAPI template.
R-graph-gallery - A website that displays hundreds of R charts with their code
hecatomb - hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
rnaseq - RNA-seq analyses.
GermlineMutationCalling - An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files