joelnitta / iscb-targets-intro

Slides for ISCB Academy workshop "Modular, reproducible bioinformatics workflows with the targets R package"

Hello! 👋 I am a Associate Profesor at Chiba University studying ferns, an ancient and diverse lineage of vascular plants.

I am an enthusiastic adherent of reproducible data analysis, especially with R.

Please check out https://www.joelnitta.com/ for more info.

✨Repo highlights✨

R packages 📦

• canaper: Categorial analysis of neo-and paleo-endemism
• taxastand: Standardize species names across data sources
• dwctaxon: Tools for working with Darwin Core Taxon data
• rmdref: Tools for reference management in Rmarkdown
• gbfetch: Fetch sequences from GenBank

Reproducible data analysis 📈

• canopylife: Code for Nitta et al. "Life in the canopy: Community trait assessments reveal substantial functional diversity among fern epiphytes"
• moorea_filmies: Code for Nitta et al. "Ecophysiological differentiation between life stages in filmy ferns (Hymenophyllaceae)"
• japan_ferns_spatial_phy: Code for Nitta et al. "Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation"
• gameto-barcode-review: Code for Nitta & Chambers "Identifying cryptic fern gametophytes using DNA barcoding: A review"
• nectandra_ferns: Code for Nitta et al. "A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica"
• japan_ferns_review: Code for Ebihara & Nitta "An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago"
• pleurosoriopsis: Code for Ebihara et al. "Growth Dynamics of the Independent Gametophytes of Pleurorosiopsis makinoi (Polypodiaceae)"

Example code 💻

• targets_bioinfo_example: Example bioinformatics workflow with targets, conda, and docker
• targets_gapminder_example: Example data analysis workflow using R targets package
• targets_vcf_example: Example variant calling workflow using R targets package

Docker images 🐳

• entap-docker: Docker image to run EnTAP
• sqanti3-docker: Docker image to run SQANTI3
• taxastand-docker: Docker image to run taxastand
• kindel-docker: Docker image to run kindel
• hybpiper-docker: Docker image to run HybPiper

iscb-targets-intro's Issues

Remotes typo

Should be install_github