GitHub - timplab/timp

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Name		Name	Last commit message	Last commit date
Latest commit History 94 Commits
timp_illumina_data @ b21a13f		timp_illumina_data @ b21a13f
.gitignore		.gitignore
.gitmodules		.gitmodules
450k_cancer_loadin.R		450k_cancer_loadin.R
450k_cancer_loaf.R		450k_cancer_loaf.R
450k_fifty_analysis.R		450k_fifty_analysis.R
450k_for_rafa_probes.R		450k_for_rafa_probes.R
450k_general_init.R		450k_general_init.R
450k_igf2_analysis.R		450k_igf2_analysis.R
450k_instruction_table.R		450k_instruction_table.R
450k_met_analysis.R		450k_met_analysis.R
450k_michael_test.R		450k_michael_test.R
450k_package_try.R		450k_package_try.R
450k_probe_anno.R		450k_probe_anno.R
450k_probe_region.R		450k_probe_region.R
450k_remap.R		450k_remap.R
450k_remap_chroms.R		450k_remap_chroms.R
450k_remap_first.R		450k_remap_first.R
450k_timp_functions.R		450k_timp_functions.R
450k_timp_script.R		450k_timp_script.R
450k_tissue_anal.R		450k_tissue_anal.R
Illumina_CHARM.R		Illumina_CHARM.R
Illumina_GCT_Converter.pl		Illumina_GCT_Converter.pl
Illumina_MATLAB_CSV_Converter.pl		Illumina_MATLAB_CSV_Converter.pl
Illumina_annotation.R		Illumina_annotation.R
Illumina_cluster.R		Illumina_cluster.R
Illumina_controls.R		Illumina_controls.R
Illumina_dataload.R		Illumina_dataload.R
Illumina_density.R		Illumina_density.R
Illumina_indivprobe.R		Illumina_indivprobe.R
Illumina_iowa_plots.R		Illumina_iowa_plots.R
Illumina_preprocess.R		Illumina_preprocess.R
Illumina_probenfo.R		Illumina_probenfo.R
Illumina_sample.R		Illumina_sample.R
Illumina_sample_annotator.pl		Illumina_sample_annotator.pl
Illumina_thyroid_plots.R		Illumina_thyroid_plots.R
Illumina_varscore.R		Illumina_varscore.R
Illumina_yia_plots.R		Illumina_yia_plots.R
MichaelregionFinder.R		MichaelregionFinder.R
OU_model.R		OU_model.R
Probe2fasta.pl		Probe2fasta.pl
README		README
Rafa_functions.R		Rafa_functions.R
SSA_meth.R		SSA_meth.R
ball_model.R		ball_model.R
biofluid_plate_maker.R		biofluid_plate_maker.R
classcompare_sub.m		classcompare_sub.m
clustergram_plot.m		clustergram_plot.m
cut_geneious_exports.pl		cut_geneious_exports.pl
data_extract.pl		data_extract.pl
dbSNP_label.pl		dbSNP_label.pl
dump_beta.R		dump_beta.R
ensembl_extract.pl		ensembl_extract.pl
find_illumina_ids.pl		find_illumina_ids.pl
findseq.R		findseq.R
findseq_start_end.pl		findseq_start_end.pl
genetic_plots.R		genetic_plots.R
genetic_region.R		genetic_region.R
get_probe.R		get_probe.R
hector_data_model.R		hector_data_model.R
hopkinstalk_stuff.R		hopkinstalk_stuff.R
hopkinstalk_stuff_laptop.R		hopkinstalk_stuff_laptop.R
ids_rename.pl		ids_rename.pl
illumina_cross_control.m		illumina_cross_control.m
illumina_data_load.m		illumina_data_load.m
illumina_genes_sub.m		illumina_genes_sub.m
illumina_knn.m		illumina_knn.m
illumina_label.pl		illumina_label.pl
illumina_label_final.pl		illumina_label_final.pl
illumina_label_whole.pl		illumina_label_whole.pl
illumina_methylation_control_samp.m		illumina_methylation_control_samp.m
illumina_pvalue.m		illumina_pvalue.m
illumina_svm.m		illumina_svm.m
illumina_tissue_best.m		illumina_tissue_best.m
illumina_tissue_best_p.m		illumina_tissue_best_p.m
isolate_final_illumina.pl		isolate_final_illumina.pl
isolate_good_illumina.pl		isolate_good_illumina.pl
mutation_list.R		mutation_list.R
plot_tissue_diff.m		plot_tissue_diff.m
plot_tumornormal.m		plot_tumornormal.m
plot_tumornormal_charm.m		plot_tumornormal_charm.m
plot_tumornormal_sub.m		plot_tumornormal_sub.m
pvalue_table_csv.m		pvalue_table_csv.m
rafa_island_dist.pl		rafa_island_dist.pl
rafa_plots.R		rafa_plots.R
readillBSD.R		readillBSD.R
remap_probes.R		remap_probes.R
results.R		results.R
sample_anno.R		sample_anno.R
trying_svm.R		trying_svm.R
ucsc_island_dist.pl		ucsc_island_dist.pl
volcano_plot.m		volcano_plot.m
web_illumina_custom.R		web_illumina_custom.R
yia_2012_info.R		yia_2012_info.R

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This repository is the home of various pieces of code for analyzing Illumina Beadarray Methylation Data

Most of the code is in R with Bioconductor packages, though there is some MATLAB and perl code as well.