Software for Genetic Data Analyses & Database Resources
G3: Genes|Genomes|Genetics offers an article format for high quality reports describing novel software for genetic data analyses and database resources. The editors of G3 recognize that modern genetic research requires specialized, efficient, and well-documented software, as well as access to high quality data.
The Software and Data Resources (SDR) format is succinct and follows a semi-structured template (details here) designed to make it easy for readers to understand the possibilities offered by the software and resource being presented.
Criteria for acceptance in this category includes the usefulness (i.e. is the tool/resource potentially useful for a broad community of researchers and not redundant with existing tools?), innovation, accessibility (including availability and quality of the documentation) and, in the case of software, scalability. Data resources must be made freely available in a public repository or as supplemental material (under 50MB), and in the case of software distribution we encourage the use of Open Source. Please see the Data and Reagent Policy for full details.
A Faster and More Accurate Algorithm for Calculating Population Genetics Statistics Requiring Sums of Stirling Numbers of the First Kind
Swaine L. Chen, Nico M. Temme
G3: Genes, Genomes, Genetics November 2020 10: 3959-3967; https://doi.org/10.1534/g3.120.401575
TheCellVision.org: A Database for Visualizing and Mining High-Content Cell Imaging Projects
Myra Paz David Masinas, Mojca Mattiazzi Usaj, Matej Usaj, Charles Boone, Brenda J. Andrews
G3: Genes, Genomes, Genetics November 2020 10: 3969-3976; https://doi.org/10.1534/g3.120.401570
MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations
Mitchell A. Ellison, Jennifer L. Walker, Patrick J. Ropp, Jacob D. Durrant, Karen M. Arndt
G3: Genes, Genomes, Genetics September 2020 10: 3009-3014; https://doi.org/10.1534/g3.120.401396
Ultraconserved Non-coding DNA Within Diptera and Hymenoptera
Thomas Brody, Amarendra Yavatkar, Alexander Kuzin, Ward F. Odenwald
G3: Genes, Genomes, Genetics September 2020 10: 3015-3024; https://doi.org/10.1534/g3.120.401502
CeMbio - The Caenorhabditis elegans Microbiome Resource
Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie-Anne Félix, Michael Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
G3: Genes, Genomes, Genetics September 2020 10: 3025-3039; https://doi.org/10.1534/g3.120.401309
rdmc: An Open Source R Package Implementing Convergent Adaptation Models of Lee and Coop (2017)
Silas Tittes
G3: Genes, Genomes, Genetics September 2020 10: 3041-3046; https://doi.org/10.1534/g3.120.401527
Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
Alexander F. Gileta, Jianjun Gao, Apurva S. Chitre, Hannah V. Bimschleger, Celine L. St. Pierre, Shyam Gopalakrishnan, Abraham A. Palmer
G3: Genes, Genomes, Genetics July 2020 10: 2195-2205; https://doi.org/10.1534/g3.120.401325
Meta-analysis of Diets Used in Drosophila Microbiome Research and Introduction of the Drosophila Dietary Composition Calculator (DDCC)
Danielle N. A. Lesperance, Nichole A. Broderick
G3: Genes, Genomes, Genetics July 2020 10: 2207-2211; https://doi.org/10.1534/g3.120.401235
MoBPS - Modular Breeding Program Simulator
Torsten Pook, Martin Schlather, Henner Simianer
G3: Genes, Genomes, Genetics June 2020 10: 1915-1918; https://doi.org/10.1534/g3.120.401193
The UCSF Mouse Inventory Database Application, an Open Source Web App for Sharing Mutant Mice Within a Research Community
Estelle Wall, Jonathan Scoles, Adriane Joo, Ophir Klein, Carlo Quinonez, Jeffrey O. Bush, Gail R. Martin, Diana J. Laird
G3: Genes, Genomes, Genetics May 2020 10: 1503-1510; https://doi.org/10.1534/g3.120.401086
LongQC: A Quality Control Tool for Third Generation Sequencing Long Read Data
Yoshinori Fukasawa, Luca Ermini, Hai Wang, Karen Carty, Min-Sin Cheung
G3: Genes, Genomes, Genetics April 2020 10: 1193-1196; https://doi.org/10.1534/g3.119.400864
An Automated Method To Predict Mouse Gene and Protein Sequences Using Variant Data
Peter Dornbos, Anooj A. Arkatkar, John J. LaPres
G3: Genes, Genomes, Genetics March 2020 10: 925-932; https://doi.org/10.1534/g3.119.400983
Interactively AUDIT Your Growth Curves with a Suite of R Packages
Nicolas P. J. Coutin, Guri Giaever, Corey Nislow
G3: Genes, Genomes, Genetics March 2020 10: 933-943; https://doi.org/10.1534/g3.119.400898
CGSEA: A Flexible Tool for Evaluating the Associations of Chemicals with Complex Diseases
Shiqiang Cheng, Mei Ma, Lu Zhang, Li Liu, Bolun Cheng, Xin Qi, Chujun Liang, Ping Li, Om Prakash Kafle, Yan Wen, Feng Zhang
G3: Genes, Genomes, Genetics March 2020 10: 945-949; https://doi.org/10.1534/g3.119.400945
SNP-CRISPR: A Web Tool for SNP-Specific Genome Editing
Chiao-Lin Chen, Jonathan Rodiger, Verena Chung, Raghuvir Viswanatha, Stephanie E. Mohr, Yanhui Hu, Norbert Perrimon
G3: Genes, Genomes, Genetics February 2020 10: 489-494; https://doi.org/10.1534/g3.119.400904
Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin Accessibility
Andrea Rau, Sumona P. Dhara, Ava J. Udvadia, Paul L. Auer
G3: Genes, Genomes, Genetics December 2019 9: 3953-3959; https://doi.org/10.1534/g3.119.400729
An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster
Ben J. Vincent, Gavin R. Rice, Gabriella M. Wong, William J. Glassford, Kayla I. Downs, Jessica L. Shastay, Kenechukwu Charles-Obi, Malini Natarajan, Madelaine Gogol, Julia Zeitlinger, Mark Rebeiz
G3: Genes, Genomes, Genetics December 2019 9: 3961-3972; https://doi.org/10.1534/g3.119.400788
A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data
Tom Hill, Robert L. Unckless
G3: Genes, Genomes, Genetics November 2019 9: 3575-3582; https://doi.org/10.1534/g3.119.400596=
micRocounter: Microsatellite Characterization in Genome Assemblies
Johnathan Lo, Michelle M. Jonika, Heath Blackmon
G3: Genes, Genomes, Genetics October 2019 9: 3101-3104; https://doi.org/10.1534/g3.119.400335
isqg: A Binary Framework for in Silico Quantitative Genetics
Fernando H. Toledo, Paulino Pérez-Rodríguez, José Crossa, Juan Burgueño
G3: Genes, Genomes, Genetics August 2019 9: 2425-2428; https://doi.org/10.1534/g3.119.400373
Computational Inference Software for Tetrad Assembly from Randomly Arrayed Yeast Colonies
Nikita A. Sakhanenko, Gareth A. Cromie, Aimée M. Dudley, David J. Galas
G3: Genes, Genomes, Genetics June 2019 9: 2071-2088; https://doi.org/10.1534/g3.119.400166
ARMOR: An Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data
Stephany Orjuela, Ruizhu Huang, Katharina M. Hembach, Mark D. Robinson, Charlotte Soneson
G3: Genes, Genomes, Genetics June 2019 9: 2089-2096; https://doi.org/10.1534/g3.119.400185
DPAC: A Tool for Differential Poly(A)–Cluster Usage from Poly(A)–Targeted RNAseq Data
Andrew Routh
G3: Genes, Genomes, Genetics June 2019 9: 1825-1830; https://doi.org/10.1534/g3.119.400273
An R Package for Bayesian Analysis of Multi-environment and Multi-trait Multi-environment Data for Genome-Based Prediction
Osval A. Montesinos-López, Abelardo Montesinos-López, Francisco Javier Luna-Vázquez, Fernando H. Toledo, Paulino Pérez-Rodríguez, Morten Lillemo, José Crossa
G3: Genes, Genomes, Genetics May 2019 9: 1355-1369; https://doi.org/10.1534/g3.119.400126
TSD: A Computational Tool To Study the Complex Structural Variants Using PacBio Targeted Sequencing Data
Guofeng Meng, Ying Tan, Yue Fan, Yan Wang, Guang Yang, Gregory Fanning, Yang Qiu
G3: Genes, Genomes, Genetics May 2019 9: 1371-1376; https://doi.org/10.1534/g3.118.200900
BGData - A Suite of R Packages for Genomic Analysis with Big Data
Alexander Grueneberg, Gustavo de los Campos
G3: Genes, Genomes, Genetics May 2019 9: 1377-1383; https://doi.org/10.1534/g3.119.400018
polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
Lindsay V. Clark, Alexander E. Lipka, Erik J. Sacks
G3: Genes, Genomes, Genetics March 2019 9: 663-673; https://doi.org/10.1534/g3.118.200913
pSBVB: A Versatile Simulation Tool To Evaluate Genomic Selection in Polyploid Species
María L. Zingaretti, Amparo Monfort, Miguel Pérez-Enciso
G3: Genes, Genomes, Genetics February 2019 9: 327-334; https://doi.org/10.1534/g3.118.200942
iProteinDB: An Integrative Database of Drosophila Post-translational Modifications
Yanhui Hu, Richelle Sopko, Verena Chung, Marianna Foos, Romain A. Studer, Sean D. Landry, Daniel Liu, Leonard Rabinow, Florian Gnad, Pedro Beltrao, Norbert Perrimon
G3: Genes, Genomes, Genetics January 2019 9: 1-11; https://doi.org/10.1534/g3.118.200637
OCMA: Fast, Memory-Efficient Factorization of Prohibitively Large Relationship Matrices
Zhi Xiong, Qingrun Zhang, Alexander Platt, Wenyuan Liao, Xinghua Shi, Gustavo de los Campos, Quan Long
G3: Genes, Genomes, Genetics January 2019 9: 13-19; https://doi.org/10.1534/g3.118.200908
A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication
Rishi De-Kayne, Philine G. D. Feulner
G3: Genes, Genomes, Genetics December 2018 8: 3745-3755; https://doi.org/10.1534/g3.118.200552
vqtl: An R Package for Mean-Variance QTL Mapping
Robert W. Corty, William Valdar
G3: Genes, Genomes, Genetics December 2018 8: 3757-3766; https://doi.org/10.1534/g3.118.200642
gQTL: A Web Application for QTL Analysis Using the Collaborative Cross Mouse Genetic Reference Population
Kranti Konganti, Andre Ehrlich, Ivan Rusyn, David W. Threadgill
G3: Genes, Genomes, Genetics August 2018 8: 2559-2562; https://doi.org/10.1534/g3.118.200230
Genomic Variation Among and Within Six Juglans Species
Kristian A. Stevens, Keith Woeste, Sandeep Chakraborty, Marc W. Crepeau, Charles A. Leslie, Pedro J. Martínez-García, Daniela Puiu, Jeanne Romero-Severson, Mark Coggeshall, Abhaya M. Dandekar, Daniel Kluepfel, David B. Neale, Steven L. Salzberg, Charles H. Langley
G3: Genes, Genomes, Genetics July 2018 8: 2153-2165; https://doi.org/10.1534/g3.118.200030
BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously
Yagul Pedraza-Pérez, Rodrigo Alberto Cuevas-Vede, Ángel Bernardo Canto-Gómez, Liliana López-Pliego, Rosa María Gutiérrez-Ríos, Ismael Hernández-Lucas, Gustavo Rubín-Linares, Ygnacio Martínez-Laguna, Jesús Francisco López-Olguín, Luis Ernesto Fuentes-Ramírez
G3: Genes, Genomes, Genetics July 2018 8: 2167-2172; https://doi.org/10.1534/g3.118.200220
Development of Diagnostic SNP Markers To Monitor Hybridization Between Sika Deer (Cervus nippon) and Wapiti (Cervus elaphus)
Hengxing Ba, Zhipeng Li, Yifeng Yang, Chunyi Li
G3: Genes, Genomes, Genetics July 2018 8: 2173-2179; https://doi.org/10.1534/g3.118.200417
Fast Ordered Sampling of DNA Sequence Variants
Anthony J. Greenberg
G3: Genes, Genomes, Genetics May 2018 8: 1455-1460; https://doi.org/10.1534/g3.117.300465
ARSDA: A New Approach for Storing, Transmitting and Analyzing Transcriptomic Data
Xuhua Xia
G3: Genes, Genomes, Genetics December 2017 7: 3839-3848; https://doi.org/10.1534/g3.117.300271
rSalvador: An R Package for the Fluctuation Experiment
Qi Zheng
G3: Genes, Genomes, Genetics December 2017 7: 3849-3856; https://doi.org/10.1534/g3.117.300120