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followers: 62.0 following: 0.0 repos: 170.0 gists: 52.0

Name: Joel Nitta

Type: User

Company: Chiba University

Bio: Associate Professor at Chiba University, Japan

Location: Tokyo, Japan

Blog: https://joelnitta.com

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

fssgam

Code for full subsets model fitting using GA(M)M

ftol_ppg_figs

gameto-barcode-review

Identifying cryptic fern gametophytes using DNA barcoding: A review

gameto_barcode_ifs

Slides for the presentation "DNA Barcoding of Fern Gametophytes: Past, Present, and Future"

gap-term-2023

gap-term-2024

Slides for Gap Term 2024 class

gbfetch

Fetch! (GenBank sequences)

git-novice

Version Control with Git

git-novice-uk

glosario

A multilingual glossary for computing and data science terms.

gni

A fork of https://github.com/GlobalNamesArchitecture/gni

graduation_thesis

harts_tongue_comment

hybphaser

Workflow to detect and phase hybrids in target capture data

hybpiper

Recovering genes from targeted sequence capture data

hybpiper-docker

Dockerfile for running HybPiper

i18n

Where all the translations are controlled from.

iscb-targets-intro

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

ismb_2022

Presentation for ISMB 2022

japan_ferns_review

An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago

japan_ferns_spatial_phy

Spatial phylogenetics of Japanese ferns

japan_ferns_spatial_phy_cache

Targets data cache for japan_ferns_spatial_phy

ja_ferns_names

Demo workflow of taxastand to resolve names of Japanese ferns

jntools

Various and sundry tools for data analysis in R

jn_cv

Academic CV Written in R Markdown

joelnitta

About Joel Nitta

joelnitta-cv

https://github.com/joelnitta/joelnitta-cv/blob/main/cv.pdf

joelnitta-home

Personal website of Joel Nitta

joelnitta-site

Personal website of Joel Nitta

joelnitta.github.io

Default website

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