R/qtl: QTL Mapping in Experimental Crosses

By Karl W. Broman, Hao Wu, Śaunak Sen, Gary A. Churchill. Bioinform., 2003

3,347 citations recorded by the source corpus.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/5cfa5bee56104c096ec321c729b403540d8c297d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Julian Catchen
2. M. Sorrells
3. Jean-Luc Jannink
4. Paul A Hohenlohe
5. E. Heffner
6. R. Singh
7. Kazuki Saito
8. Miguel Andrade

In Plant Science

1. M. Sorrells
2. Jean-Luc Jannink
3. Julian Catchen
4. R. Singh
5. E. Heffner
6. G. Velu
7. Yuanfeng Hao
8. A. Yazi̇ci̇

Citations in the corpus

• Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences (2011, methodology): “At this point, Stacks calls genotypes from map cross progeny using genotypes.pl after specifying a particular map type (F1, F2, doubled haploid, or back cross) and an export type (JoinMap or R/qtl).”
• Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals (2017, methodology): “QTL analysis was performed using R/qtl package (Broman et al., 2003) selecting the following traits obtained from GeneNetwork: INIA Amygdala Cohort Affy MoGene 1 0 ST Mar11 RMA, UTH SC Mouse BXD Whole Brain RNA Sequence Nov12 RPKM Untrimmed, GE NIA AA Cerebellum mRNA M430v2 May05 RMA, Hippocampus Co”
• Marker-Assisted Plant Breeding: Principles and Practices (2015, neutral): “214 7.19.5 R/QTL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214 7.19.6 R/QTLBIM . . . . . . . . . . . . . . . . . . . . . . . . . .”
• Matrix eQTL: ultra fast eQTL analysis via large matrix operations (2011, methodology): “We compare performance of Matrix eQTL with that of five programs for QTL and eQTL analysis: Plink [Purcell et al., 2007], Merlin [Abecasis et al., 2001], R/qtl [Broman et al., 2003], eMap [Sun, 2009], and FastMap Gatti et al. [2009, 2011].”
• Deep machine learning provides state-of-the-art performance in image-based plant phenotyping (2016, positive): “Outputs of the analysis program R/qtl [21] are summarized in Table 4.”
• QGene 4.0, an extensible Java QTL-analysis platform (2008, neutral): “Of the software listed above, R/qtl, essentially a function library written in the popular multi-platform statistical and graphical language R, is the most extensible.”
• Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function (2005, methodology): “We carried out pair-wise QTL scanning for epistasis for a small number of selected transcripts using R/qt”
• JCVI: A versatile toolkit for comparative genomics analysis (2024, methodology): “To overcome these obstacles, one approach, exemplified by earlier map ‐ based software including JoinMap, MSTMap, and R/qtl, capitalizes on the synergies between genome sequencing and linkage mapping [38 – 40].”
• Potent Induction of Arabidopsis thaliana Flowering by Elevated Growth Temperature (2006, positive): “QTL mapping was performed using R-qtl [71].”