Other packages > Find by keyword >

qtl2  

Quantitative Trait Locus Mapping in Experimental Crosses
View on CRAN: Click here


Download and install qtl2 package within the R console
Install from CRAN:
install.packages("qtl2")

Install from Github:
library("remotes")
install_github("cran/qtl2")

Install by package version:
library("remotes")
install_version("qtl2", "0.46")



Attach the package and use:
library("qtl2")
Maintained by
Karl W Broman
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-06-26
Latest Update: 2025-06-02
Description:
Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) .
How to cite:
Karl W Broman (2020). qtl2: Quantitative Trait Locus Mapping in Experimental Crosses. R package version 0.46, https://cran.r-project.org/web/packages/qtl2. Accessed 05 Oct. 2026.
Previous versions and publish date:
(2026-07-21 14:30), 0.22-8 (2020-06-26 12:40), 0.22-11 (2020-07-10 17:50), 0.24 (2020-12-18 17:30), 0.28 (2021-10-17 22:20), 0.30 (2022-12-02 16:10), 0.32 (2023-04-22 02:52), 0.34 (2023-11-28 23:40), 0.36 (2024-05-13 16:30), 0.38 (2025-06-02 15:00), 0.40 (2026-05-04 23:10), 0.42 (2026-06-09 05:20), 0.44 (2026-07-06 16:10)
Other packages that cited qtl2 R package
View qtl2 citation profile
Other R packages that qtl2 depends, imports, suggests or enhances
Complete documentation for qtl2
Functions, R codes and Examples using the qtl2 R package
Some associated functions: CCcolors . add_threshold . basic_summaries . batch_cols . batch_vec . bayes_int . calc_entropy . calc_errorlod . calc_geno_freq . calc_genoprob . calc_grid . calc_het . calc_kinship . calc_raw_founder_maf . calc_raw_geno_freq . calc_raw_het . calc_raw_maf . calc_sdp . cbind.calc_genoprob . cbind.scan1 . cbind.scan1perm . cbind.sim_geno . cbind.viterbi . cbind_expand . check_cross2 . chisq_colpairs . chr_lengths . clean . clean_genoprob . clean_scan1 . compare_geno . compare_genoprob . compare_maps . convert2cross2 . count_xo . create_gene_query_func . create_snpinfo . create_variant_query_func . decomp_kinship . drop_markers . drop_nullmarkers . est_herit . est_map . find_dup_markers . find_ibd_segments . find_index_snp . find_map_gaps . find_marker . find_markerpos . find_peaks . fit1 . fread_csv . fread_csv_numer . genoprob_to_alleleprob . genoprob_to_snpprob . get_common_ids . get_x_covar . guess_phase . index_snps . insert_pseudomarkers . interp_genoprob . interp_map . invert_sdp . locate_xo . lod_int . map_to_grid . mat2strata . max_compare_geno . max_scan1 . maxlod . maxmarg . n_missing . plot_coef . plot_compare_geno . plot_genes . plot_genoprob . plot_genoprobcomp . plot_lodpeaks . plot_onegeno . plot_peaks . plot_pxg . plot_scan1 . plot_sdp . plot_snpasso . predict_snpgeno . print.cross2 . print.summary.scan1perm . probs_to_grid . pull_genoprobint . pull_genoprobpos . pull_markers . qtl2-internal . qtl2-package . qtl2version . rbind.calc_genoprob . rbind.scan1 . rbind.scan1perm . rbind.sim_geno . rbind.viterbi . read_cross2 . read_pheno . recode_snps . reduce_map_gaps . reduce_markers . replace_ids . scale_kinship . scan1 . scan1blup . scan1coef . scan1max . scan1perm . scan1snps . sdp2char . sim_geno . smooth_gmap . subset.calc_genoprob . subset.cross2 . subset.sim_geno . subset.viterbi . subset_scan1 . summary.cross2 . summary_compare_geno . summary_scan1perm . top_snps . unsmooth_gmap . viterbi . write_control_file . xpos_scan1 . zip_datafiles . 
Some associated R codes: CCcolors-data.R . RcppExports.R . add_threshold.R . align_scan1_map.R . arg_util.R . assign_allele_codes.R . batch_cols.R . batch_vec.R . bayes_int.R . calc_entropy.R . calc_errorlod.R . calc_geno_freq.R . calc_genoprob.R . calc_genoprob2.R . calc_grid.R . calc_het.R . calc_kinship.R . calc_raw_summaries.R . calc_sdp.R . cbind_calc_genoprob.R . cbind_expand.R . cbind_scan1.R . cbind_sim_geno.R . cbind_viterbi.R . check_cross2.R . chisq_colpairs.R . chr_lengths.R . clean.R . clean_genoprob.R . clean_scan1.R . cluster_util.R . compare_geno.R . compare_genoprob.R . compare_maps.R . convert2cross2.R . count_xo.R . covariates.R . create_gene_query_func.R . create_marker_index.R . create_snpinfo.R . create_variant_query_func.R . decomp_kinship.R . dim_calc_genoprob.R . drop_markers.R . est_herit.R . est_map.R . find_common_ids.R . find_dup_markers.R . find_ibd_segments.R . find_index_snp.R . find_map_gaps.R . find_marker.R . find_markerpos.R . find_peaks.R . find_peaks_and_bayesint.R . find_peaks_and_lodint.R . fit1.R . fit1_pg.R . fread_csv.R . fread_csv_numer.R . genoprob_col2drop.R . genoprob_to_alleleprob.R . genoprob_to_snpprob.R . get_common_ids.R . get_x_covar.R . guess_phase.R . hmm_util.R . index_snps.R . insert_pseudomarkers.R . interp_genoprob.R . interp_map.R . is_phase_known.R . is_same.R . kinship_util.R . locate_xo.R . lod_int.R . map_functions.R . map_to_grid.R . mat2strata.R . max_scan1.R . maxmarg.R . myround.R . n_missing.R . plot_coef.R . plot_coef_and_lod.R . plot_genes.R . plot_genoprob.R . plot_genoprobcomp.R . plot_lodpeaks.R . plot_onegeno.R . plot_peaks.R . plot_pxg.R . plot_scan1.R . plot_sdp.R . plot_snpasso.R . plot_snpasso_and_genes.R . plot_snpasso_and_sdp.R . plot_snpasso_sdp_and_genes.R . predict_snpgeno.R . probs_to_grid.R . pull_genoprobint.R . pull_genoprobpos.R . qtl2-internal.R . qtl2-package.R . qtl2version.R . rbind_calc_genoprob.R . rbind_scan1.R . rbind_sim_geno.R . rbind_viterbi.R . rcbind_scan1perm.R . read_cross2.R . read_pheno.R . recode_snps.R . reduce_map_gaps.R . reduce_markers.R . reduce_to_index_snps.R . replace_ids.R . scale_kinship.R . scan1.R . scan1_binary.R . scan1_pg.R . scan1blup.R . scan1blup_pg.R . scan1coef.R . scan1coef_pg.R . scan1max.R . scan1max_pg.R . scan1perm.R . scan1perm_pg.R . scan1snps.R . sim_geno.R . sim_geno2.R . smooth_gmap.R . snpprob_from_cross.R . subset_calc_genoprob.R . subset_chr.R . subset_cross2.R . subset_ind.R . subset_kinship.R . subset_scan1.R . subset_sim_geno.R . subset_viterbi.R . summary_cross2.R . summary_scan1perm.R . swap_colname.R . test_util.R . top_snps.R . unsmooth_gmap.R . viridis.R . viterbi.R . viterbi2.R . weights_util.R . write_control_file.R . xpos_scan1.R . zip_datafiles.R .  Full qtl2 package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

genie  
Fast, Robust, and Outlier Resistant Hierarchical Clustering
Includes the reference implementation of Genie - a hierarchical clustering algorithm that links two ...
Download / Learn more Package Citations See dependency  
correlation  
Methods for Correlation Analysis
Lightweight package for computing different kinds of correlations, such as partial correlations, Ba ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
cdlTools  
Tools to Download and Work with USDA Cropscape Data
Downloads USDA National Agricultural Statistics Service (NASS) cropscape data for a specified state ...
Download / Learn more Package Citations See dependency  

28,905

R Packages

247,686

Dependencies

76,495

Author Associations

28,906

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA