GitHub - cjieming2/R_Codes: This is a sandbox of scripts that I have created (~98%) or gathered from others since 2007. It is only stored here for utility and posterity. They are all constantly being updated, thus they should be treated as work-in-progress - raw and unpolished. Please ask for permission before publishing.

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This is a sandbox of scripts that I have created (~98%) or gathered from others since 2007. It is only stored here for utility and posterity. They are all constantly being updated, thus they should be treated as work-in-progress - raw and unpolished. Please ask for permission before publishing.

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Name		Name	Last commit message	Last commit date
Latest commit History 23 Commits
PubMed		PubMed
PubMedTrend_2011		PubMedTrend_2011
manual plot		manual plot
obsolete		obsolete
plotting genomics course		plotting genomics course
polnet2017_networks_tutorial		polnet2017_networks_tutorial
project_motifVar_enrichment_blosum_sift		project_motifVar_enrichment_blosum_sift
.DS_Store		.DS_Store
CSQPlot.R		CSQPlot.R
DiscriminantAnalysis_RScript_JRS.r		DiscriminantAnalysis_RScript_JRS.r
Factor+Analysis.R		Factor+Analysis.R
HartiganROT1.R		HartiganROT1.R
NA		NA
README		README
Rscript-analyze- PCA-with-HapMap-samples.R		Rscript-analyze- PCA-with-HapMap-samples.R
adrian_pca.r		adrian_pca.r
adrian_pca1.r		adrian_pca1.r
adrian_relatives.r		adrian_relatives.r
allelePeak_binomial.r		allelePeak_binomial.r
allele_betabinomial_minN.R		allele_betabinomial_minN.R
allele_betabinomial_minN_single_solo_dataset.R		allele_betabinomial_minN_single_solo_dataset.R
allele_betabinomial_plot.R		allele_betabinomial_plot.R
allele_binomial.R		allele_binomial.R
allele_bins_barplots_deprecated.r		allele_bins_barplots_deprecated.r
allele_boxplot_indiv.R		allele_boxplot_indiv.R
allele_confident_set.R		allele_confident_set.R
allele_coverage_hist_deprecated.R		allele_coverage_hist_deprecated.R
allele_depth_intHets_hist_acc_intHets_notSubset-fig.R		allele_depth_intHets_hist_acc_intHets_notSubset-fig.R
allele_depth_intHets_hist_asb-fig.R		allele_depth_intHets_hist_asb-fig.R
allele_depth_intHets_hist_ase-fig.R		allele_depth_intHets_hist_ase-fig.R
allele_depth_intHets_hist_v2.R		allele_depth_intHets_hist_v2.R
allele_enrichment_barplots-fig.r		allele_enrichment_barplots-fig.r
allele_enrichment_barplots.r		allele_enrichment_barplots.r
allele_enrichment_thermometer-fig.r		allele_enrichment_thermometer-fig.r
allele_info_pooled_int_acc_counts.transparent.figure.r		allele_info_pooled_int_acc_counts.transparent.figure.r
allele_info_rship_plots.R		allele_info_rship_plots.R
allele_inheritance_asbe_figure.R		allele_inheritance_asbe_figure.R
allele_inheritance_asbe_quantify_corr_slope.fig.R		allele_inheritance_asbe_quantify_corr_slope.fig.R
allele_inheritance_asbe_quantify_indiv.R		allele_inheritance_asbe_quantify_indiv.R
allele_inheritance_asbe_quantify_indiv_quadrantfig.R		allele_inheritance_asbe_quantify_indiv_quadrantfig.R
allele_motif_analyses.R		allele_motif_analyses.R
allele_newpeaks_cnved.R		allele_newpeaks_cnved.R
allele_numIndiv_pseudogenes.r		allele_numIndiv_pseudogenes.r
allele_plot_allelefreq-fig.R		allele_plot_allelefreq-fig.R
allele_plot_allelefreq.pop.R		allele_plot_allelefreq.pop.R
allele_plot_sharing.R		allele_plot_sharing.R
allele_readdepth_plot_b_compare_grad.R		allele_readdepth_plot_b_compare_grad.R
allele_readdepth_plot_b_grad.R		allele_readdepth_plot_b_grad.R
allele_readdepth_table_beta&binomial_distribution_compare.R		allele_readdepth_table_beta&binomial_distribution_compare.R
allele_readdepth_table_beta&binomial_distribution_gradient.R		allele_readdepth_table_beta&binomial_distribution_gradient.R
allele_readdepth_table_binomial_distribution_compare.R		allele_readdepth_table_binomial_distribution_compare.R
allele_readdepth_table_binomial_distribution_compare_hist.R		allele_readdepth_table_binomial_distribution_compare_hist.R
allele_reference_bias_plot.R		allele_reference_bias_plot.R
allele_reference_good_and_bad_overdispersion.figure.R		allele_reference_good_and_bad_overdispersion.figure.R
allele_snps_chrhist.R		allele_snps_chrhist.R
allele_tf-assoc.r		allele_tf-assoc.r
allele_vennDiagram.R		allele_vennDiagram.R
alleleseq_in_betabinomial.R		alleleseq_in_betabinomial.R
bayesian_stat645_final.R		bayesian_stat645_final.R
binomtest_allelePeak.r		binomtest_allelePeak.r
binomtest_fig.r		binomtest_fig.r
biplot-hsa.r		biplot-hsa.r
chisqquantileplot.r		chisqquantileplot.r
ciscoreplot.R.txt-1.R		ciscoreplot.R.txt-1.R
clipplot-threshold colors.r		clipplot-threshold colors.r
cluster_analysis_with_dataset_stat660.R		cluster_analysis_with_dataset_stat660.R
cong_Bayesian.R		cong_Bayesian.R
cong_hmm.R		cong_hmm.R
correlation_all.r		correlation_all.r
defense_sequencingCost.R		defense_sequencingCost.R
dreeves_convert_gene_probes.R		dreeves_convert_gene_probes.R
dreeves_hw3.R		dreeves_hw3.R
erwin-pcaPlot-greying-simul.R		erwin-pcaPlot-greying-simul.R
fdr.R		fdr.R
fdr_cbb_yale.R		fdr_cbb_yale.R
fig_change_cat_names_fromYao.r		fig_change_cat_names_fromYao.r
filter_input_table_for_network.txt		filter_input_table_for_network.txt
findDuplicates.r		findDuplicates.r
fisherstest.r		fisherstest.r
fitting_rebecca.R		fitting_rebecca.R
ggplot_stat_function.Rmd		ggplot_stat_function.Rmd
ggplot_stat_function.nb.html		ggplot_stat_function.nb.html
graph4ekta.r		graph4ekta.r
graphics_in_R.Rmd		graphics_in_R.Rmd
graphics_in_R.nb.html		graphics_in_R.nb.html
hartiganROT.R		hartiganROT.R
hartiganROT2.r		hartiganROT2.r
heterozygosityPlot-w-identify-code.r		heterozygosityPlot-w-identify-code.r
hmm_stat645_final.R		hmm_stat645_final.R
immport_connect.R		immport_connect.R
immport_initial_commands.R		immport_initial_commands.R
jmRlib.R		jmRlib.R
karseng-Manhattan-Plot-With-Limits-pvalues.r		karseng-Manhattan-Plot-With-Limits-pvalues.r
karseng-plotPCA-Highlight-Ind-Population.r		karseng-plotPCA-Highlight-Ind-Population.r
kstest.R		kstest.R
kstest_mannwhitney.R		kstest_mannwhitney.R
manova_glm_with_dataset_finalproj_stat660.R		manova_glm_with_dataset_finalproj_stat660.R
manova_glm_with_dataset_stat660.R		manova_glm_with_dataset_stat660.R
matthew_Patient-overlap-in-AD-studies2.R		matthew_Patient-overlap-in-AD-studies2.R
matthew_Patient-overlap-jcedited.R		matthew_Patient-overlap-jcedited.R

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//**[NOTE: this was originally with my old account 'cjieming', which turned defunct due to login issues. Any further updates will reside here]**// This is a sandbox of scripts that I have created (~98%) or gathered from others since 2007. It is only stored here for utility and posterity. They are all constantly being updated, thus they should be treated as work-in-progress - raw and unpolished. Please ask for permission before publishing.