danforthcenter/bioinformatics

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Created over 8 years ago
Updated over 4 years ago

danforthcenter/bioinformatics

danforthcenter

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The Donald Danforth Plant Science Center Bioinformatics Core Facility public repository

plantcv

Plant phenotyping with image analysis

plantcv-workshop

PlantCV Workshops

Jupyter Notebook

plantcv-v2-paper

PlantCV image analysis scripts used in the PlantCV v2.0 paper

Jupyter Notebook

apps-phenotyping

The following are scripts and instruction necessary to set up 4 Raspberry Pi Powered Imaging Platforms

Jupyter Notebook

plantcv-binder

A repository for interactive PlantCV documentation using Binder

Jupyter Notebook

outreach

Repository for Outreach Activities at DDPSC

phenome2020-workshop

Phenome 2020 Digital Phenotyping workshop materials

Jupyter Notebook

plantcv-tutorial-v4-VIS-single-plant

PlantCV Tutorial using release-4.0 for single plant, VIS image (RGB) analysis

Jupyter Notebook

plantcv-nappn2021-workshop

NAPPN 2021 Conference PlantCV virtual workshop materials

Jupyter Notebook

pcvr

R functions for use with plantCV output

htcondor-tools

A collection of scripts for building and running HTCondor jobs and workflows

plantcv-seeds

Seed phenotyping with PlantCV

Jupyter Notebook

plantcv-tutorial_leaf_instance_segmentation

Jupyter Notebook

plantcv-tutorial-morphology

Jupyter Notebook

brachypodium-heat-drought-paper

PlantCV python scripts for image analysis; R scripts for data filtering, organizing, and analysis; shell scripts for SNP calling and population structure estimation; input data files for all analyses

plantcv-stomata-tutorial

interactive tutorial for analyzing microscopy images of stomata using PlantCV

Jupyter Notebook

plantcv-tutorial-pollen-germination

Jupyter Notebook

plantcv-dev-scripts

Development image analysis scripts

plantcv-tasselyzer-tutorial

Jupyter Notebook

persistent_homology

Persistent homology

quinoa-pollen-germination

plantcv-annotate

add-on package for PlantCV annotation tools

Eveland_NSF_Outreach

Repository for Outreach Activities

Jupyter Notebook

plantcv-tutorial-germination

Notebook for performing germination studies using plantCV

Jupyter Notebook

plantcv-tutorial-watershed

watershed tutorial

Jupyter Notebook

UFMG-PlantCV-Workshop

Jupyter Notebook

plantcv-terra

PlantCV scripts for analyzing data from the TERRA-REF project

Jupyter Notebook

plantcv-tutorial-threshold

Tutorial for understanding Thresholding using PlantCV.

Jupyter Notebook

plantcvR

plantcv-tutorial-seeds

seed workflow tutorial

Jupyter Notebook

FiReMAGE

data-science-tools

Data Science Tools

quinoa-trait

Gehan Lab Shiny App to Explore Quinoa Phenotype Data

diel-explorer

Gehan Lab shiny app to graph JTK Cycle Output

pgwasdbc

R Package that handles and maintains a connection to GWAS database.

plantcv-hyperspectral

Hyperspectral analysis tools in PlantCV

plantcv-setaria-molplant

PlantCV image analysis scripts used in Fahlgren N, Feldman M, Gehan MA, Wilson MS, Shyu C, Bryant DW, et al. A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria. Mol Plant. 2015;8: 1520–1535.

plantcv-tutorial-hyperspectral-smf-detection

Jupyter Notebook

plantcv-geospatial

Geospatial add-on package to PlantCV

heritable-highCO2-response