1,482 Works

Quantitative Genetics of the Maize Phyllosphere

Jason Wallace, Karl Kremling & Edward S. Buckler
Bioinfromatic scripts and key intermediate files for analysis of the maize Phyllosphere from ~300 diverse inbred maize lines grown in Aurora, New York in the summer of 2014. Support dataset for Wallace et al. 2018, "Quantitative genetics of the maize leaf microbiome."
Note: v1.1 added scripts used for a simulation analysis requested in revisions.

Genetic variation and GWAS annotation

William Palmer
Code to calculate genetic variation, heritability, and genetic correlations from Kallithea titre and mortality in DGRP lines. Also will take GWAS output and make annotation tables and perform GO term analysis.

floating11.c

floating

phi_toolbox.zip

Masafumi Oizumi & Jun Kitazono
MATLAB codes for computing practical measures of integrated information proposed in Oizumi et al., 2016, PLoS Comp Biol and Oizumi et al., 2016, PNAS.
Oizumi, M., Amari, S., Yanagawa, T., Fujii, N., & Tsuchiya, N. (2016). Measuring integrated information from the decoding perspective. PLoS Comput Biol, 12(1), e1004654. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004654
Oizumi, M., Tsuchiya, N., & Amari, S. (2016). Unified framework for information integration based on information geometry. Proceedings of the National Academy of Sciences, 113(51), 14817-14822. http://www.pnas.org/content/113/51/14817.short

Practical PHI Toolbox

Jun Kitazono & Masafumi Oizumi
This MATLAB toolbox provides codes for computing practical measures of integrated information proposed in Oizumi et al., 2016, PLoS Comp Biol and Oizumi et al., 2016, PNAS and codes for efficiently searching the Minimum Information Partition (MIP) proposed in Hidaka & Oizumi, 2018, PLoS ONE and Kitazono et al., 2018, Entropy (Queyranne’s algorithm). Please see Readme.docx for more details. The codes for Queyranne’s algorithm were written by Shohei Hidaka at JAIST (Japan Advanced Institute of...

Practical PHI Toolbox

Jun Kitazono & Masafumi Oizumi
This MATLAB toolbox provides codes for computing practical measures of integrated information proposed in Oizumi et al., 2016, PLoS Comp Biol and Oizumi et al., 2016, PNAS and codes for efficiently searching the Minimum Information Partition (MIP) proposed in Hidaka et al., 2018, PLoS ONE and Kitazono et al., 2018, Entropy (Queyranne’s algorithm). Please see Readme.docx for more details. The codes for Queyranne’s algorithm were written by Shohei Hidaka at JAIST (Japan Advanced Institute of...

GrainSizeTools script v2.0.2 JOSS submission

Marco A. Lopez-Sanchez
GrainSizeTools is a free, open-source, cross-platform script written in Python that provides several tools to estimate the average grain size in polycrystalline materials, characterize the nature of the distribution of grain sizes (apparent and approximate 3D grain size distributions via stereology), and estimate the differential stress via paleopizometers. The script requires as the input the areas of the grain profiles measured grain-by-grain on planar sections and does not require previous experience with Python programming language...

SAI macros, 11.2018

Tetsuhiro Asada
ImageJ macros used in DOI.####

Adult low pH exposure influences larval abundance in Pacific oysters (Crassostrea gigas)

Supplement for the paper "Adult low pH exposure influences larval abundance in Pacific oysters (Crassostrea gigas)." This repository includes histology images, raw data for seawater chemistry, gonad maturation, and larval abundance, and code for final analyses and images.
ABSTRACT: As negative effects of ocean acidification are experienced by coastal ecosystems, there is a growing trend to investigate the effect ocean acidification has on multiple generations. Parental exposure to ocean acidification has been shown to induce larval...

body_nims_dwm_sample_method.sql.txt

Christopher Woodall
Please see readme text for how this SQL code works with FIA public data and Woodall et al. Scientific Data publication

package_nims_dwm.sql.txt

Christopher Woodall
Please see readme text for how this SQL code works with FIA public data and Woodall et al. Scientific Data publication

package_nims_stratum_sample_ratios.sql.txt

Christopher Woodall
Please see readme text for how this SQL code works with FIA public data and Woodall et al. Scientific Data publication

package_nims_dwm.sql.txt

Christopher Woodall
Please see readme text for how this SQL code works with FIA public data and Woodall et al. Scientific Data publication

Lionfish metapopulation paper - R code

Isabelle Cote
R code for Tamburello et al MS submitted to Phil Trans Roy Soc B

R code for scRNA-seq data processing

R code for scRNA-seq data processing

Assem's Arabic Stemmer

Assem Chelli
Assem's Arabic Light Stemmer is a snowball-based stemming algorithm for Arabic aimed mainly to improve search.

Dedalus Code from Generalized quasilinear approximation of the interaction of convection and mean flows in a thermal annulus

, &
This Dedalus code integrates the relevant equations

Chalkowskietal_Rcode_29SEP2018.R

Kayleigh Chalkowski
created from literature search in web of science and google scholar following PRISMA guidelines

resistorColCalc

A Resistance Calculator

Deep_Localization_code.zip

Liu Kan
Software of three-dimensional localization microscopy

AO-347029_PolySpec-Examples

Steven Wagner
PolySpec examples (compatible to Matlab and GNU Octave) and simulation data files.

9. Build a new indicator . PGI.ipynb

Simon Porter
This Jupyter notebook demonstrates how to build a new indicator using the Dimensions API

6. Citation Graph example.ipynb

Simon Porter
A Jupyter notebook that demonstrates how to make a citation graph using the Dimensions API

5. Citations by year of citation.ipynb

Simon Porter
A Jupyter notebook that shows how to get citations by year of citation from the Dimensions API

7. International linkages collaboration Tutorial.ipynb

Simon Porter
A Jupyter notebook that demonstrates how to make an international linkages graph at the institutional level

Registration Year

  • 2018
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Resource Types

  • Software
    1,482