joelnitta Goto Github PK

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Name: Joel Nitta

Type: User

Company: Chiba University

Bio: Associate Professor at Chiba University, Japan

Location: Tokyo, Japan

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

Joel Nitta's Projects

.github

2020-09-21-swc

Demo lesson page for teaching software carpentry

2021-04-02-todai-online-ja

ソフトウェアカーペントリー・ワークショップのウェブサイト

2021-04-02-todai-slides

Rによるデータ解析入門

2022-biocasia_targets

Introduction to BioC Asia and how to use {targets} for effective workflows in R

alignwise

alignwise-docker

antrophyum_ow

Code to run biogeographic analyses for Chen et al. "Systematics and biogeography of the Old World fern genus Antrophyum"

asiar-targets-intro

Introduction to the {targets} R pacakge at Asia-R meetup

assessment-archives

An archive of all the versions of the Carpentries surveys

awesome-cv-docker

Dockerized compilation of Awesome-CV-based documents

babelquarto

Renders a Multilingual Quarto Project (Book or Website)

babelwhale

Talking to Docker and Singularity containers

baitfindr

Find baits using the Yang and Smith (2014) phylogenomic analysis pipeline

baitfindr-docker

Docker image for baitfindR

baitfindr_example

Example of how to use baitfindR

binder-test

bioc_cab_2023-07-14

Presentation on translation for Bioconductor CAB

bioconda-recipes

Conda recipes for the bioconda channel.

biodigi_2022

Presentation for BioDigiCon2022

biodiverse_pipeline

Biodiverse pipeline for automating Biodiverse using R

biogeobears

BioGeography with Bayesian (and likelihood) Evolutionary Analysis with R Scripts

bioinfo-book-club

「バイオインフォマティクスデータスキル」輪読会のメモ

bioinfo_skills_2021-07-12

Slides for "Bioinformatics Data Skills" reading group talk

biopack-targets-intro

Presentation about {targets} R package for biopackathon meetup

biopack_2024-02-17

Slides for presentation at Bio"Pack"athon 2024 #2

biopak-ropen-2023-06-14

Slides for BioPackathon 2023-06-14

blast-docker

booklist

R package to maintain a book list with Zotero and Google Sheets

botany_2022_ftol

Slides for Botany 2022 presentation on the Fern Tree of Life (FTOL)