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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", "0.38")



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 0.38, https://cran.r-project.org/web/packages/qtl2. Accessed 25 Jun. 2026.
Previous versions and publish date:
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)
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
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