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This repository includes my personal Rscripts. These codes were written for different analysis as part of various bioinformatics pipelines.

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Name		Name	Last commit message	Last commit date
Latest commit History 69 Commits
Amino_acid_imp_code_from_Adrian		Amino_acid_imp_code_from_Adrian
Amino_acid_imp_code_from_Felicity		Amino_acid_imp_code_from_Felicity
ManagementZoneML-master/ManagementZoneML-master		ManagementZoneML-master/ManagementZoneML-master
WashU_codes		WashU_codes
image_analysis/MASTER R CODES		image_analysis/MASTER R CODES
letter_Prokopenko		letter_Prokopenko
#Analyse_project_MERGE_accumulate_mode.r#		#Analyse_project_MERGE_accumulate_mode.r#
#Analyse_project_concatinate_tst_files.r#		#Analyse_project_concatinate_tst_files.r#
#Apply inheritance QC_MUILT_NEW_PCA_ULTRA.v1.r#		#Apply inheritance QC_MUILT_NEW_PCA_ULTRA.v1.r#
#genotype.components.4.skatmeta.LEO.r#		#genotype.components.4.skatmeta.LEO.r#
#locus_zoom_plot.r#		#locus_zoom_plot.r#
.gitignore		.gitignore
2015-02-11_LeoPharmFinalAnalysisRedoChr1.plink_file_merge.txt		2015-02-11_LeoPharmFinalAnalysisRedoChr1.plink_file_merge.txt
2015-02-11_LeoPharmFinalAnalysis_plink_0.bed		2015-02-11_LeoPharmFinalAnalysis_plink_0.bed
2015-02-11_LeoPharmFinalAnalysis_plink_0.bim		2015-02-11_LeoPharmFinalAnalysis_plink_0.bim
2015-02-11_LeoPharmFinalAnalysis_plink_0.fam		2015-02-11_LeoPharmFinalAnalysis_plink_0.fam
AH84IQ~G.TXT		AH84IQ~G.TXT
ALL_eth_650Y_forward_hg19_Best.bim		ALL_eth_650Y_forward_hg19_Best.bim
AOGC-FN-replication.txt		AOGC-FN-replication.txt
AOGC-FN-replication.xlsx		AOGC-FN-replication.xlsx
AOGC-LS-replication.txt		AOGC-LS-replication.txt
AOGC-LS-replication.xlsx		AOGC-LS-replication.xlsx
AOGC_example.r		AOGC_example.r
AOGC_subset_on_genes.txt		AOGC_subset_on_genes.txt
AOGC_subset_on_genes_summary_stats.txt		AOGC_subset_on_genes_summary_stats.txt
ASAS_analysis_sept4Z_2015.r		ASAS_analysis_sept4Z_2015.r
AS_heatmap_dendro.jpeg		AS_heatmap_dendro.jpeg
Analyse_QQs_ExomeChip.R		Analyse_QQs_ExomeChip.R
Analyse_project_LARGE_FILE_READ.template.r		Analyse_project_LARGE_FILE_READ.template.r
Analyse_project_MERGE.r		Analyse_project_MERGE.r
Analyse_project_MERGE_AML_ANALYSIS_2015.r		Analyse_project_MERGE_AML_ANALYSIS_2015.r
Analyse_project_MERGE_AML_ANALYSIS_2015_F.r		Analyse_project_MERGE_AML_ANALYSIS_2015_F.r
Analyse_project_MERGE_AML_ANALYSIS_NEW.r		Analyse_project_MERGE_AML_ANALYSIS_NEW.r
Analyse_project_MERGE_AML_ANALYSIS_NEW_share-changedparallels.r		Analyse_project_MERGE_AML_ANALYSIS_NEW_share-changedparallels.r
Analyse_project_MERGE_AML_ANALYSIS_NEW_share.r		Analyse_project_MERGE_AML_ANALYSIS_NEW_share.r
Analyse_project_MERGE_AML_AOGC.r		Analyse_project_MERGE_AML_AOGC.r
Analyse_project_MERGE_AOGC_ANALYSIS_NEW_GEFOS_CHIP.r		Analyse_project_MERGE_AOGC_ANALYSIS_NEW_GEFOS_CHIP.r
Analyse_project_MERGE_AOGC_ANALYSIS_NEW_PAPER_CHIP.r		Analyse_project_MERGE_AOGC_ANALYSIS_NEW_PAPER_CHIP.r
Analyse_project_MERGE_AOGC_ANALYSIS_NEW_PAPER_MURCURY.r		Analyse_project_MERGE_AOGC_ANALYSIS_NEW_PAPER_MURCURY.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_FINAL.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_FINAL.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_FINALv2.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_FINALv2.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_FINALv3.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_FINALv3.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_v2.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_v2.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_v3.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_v3.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_v4.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_v4.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_v5.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_v5.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_v6.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_v6.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_v7.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_v7.r
Analyse_project_MERGE_LEO_ANALYSIS_NEW_v8.r		Analyse_project_MERGE_LEO_ANALYSIS_NEW_v8.r
Analyse_project_MERGE_LEO_New_RECOVERY.r		Analyse_project_MERGE_LEO_New_RECOVERY.r
Analyse_project_MERGE_LEO_to_AML.r		Analyse_project_MERGE_LEO_to_AML.r
Analyse_project_MERGE_LEO_to_AML_auto.r		Analyse_project_MERGE_LEO_to_AML_auto.r
Analyse_project_MERGE_NMD_ANALYSIS_NEW.r		Analyse_project_MERGE_NMD_ANALYSIS_NEW.r
Analyse_project_MERGE_NMD_cohort.r		Analyse_project_MERGE_NMD_cohort.r
Analyse_project_MERGE_accumulate_mode.r		Analyse_project_MERGE_accumulate_mode.r
Analyse_project_MERGE_accumulate_mode_AML.r		Analyse_project_MERGE_accumulate_mode_AML.r
Analyse_project_MERGE_accumulate_mode_SNPSTATS.r		Analyse_project_MERGE_accumulate_mode_SNPSTATS.r
Analyse_project_MERGE_wanted_AND_Good_Common.r		Analyse_project_MERGE_wanted_AND_Good_Common.r
Analyse_project_auto_collect_chr.r		Analyse_project_auto_collect_chr.r
Analyse_project_collect_SKAT_chromosomes.r		Analyse_project_collect_SKAT_chromosomes.r
Analyse_project_collect_results.r		Analyse_project_collect_results.r
Analyse_project_concatinate_tst_files.r		Analyse_project_concatinate_tst_files.r
Analyse_project_new.r		Analyse_project_new.r
Analyse_project_new_2015.r		Analyse_project_new_2015.r
Analyse_project_new_Aug_2014.r		Analyse_project_new_Aug_2014.r
Analyse_project_new_GENO_DUMP.AML_TEST.r		Analyse_project_new_GENO_DUMP.AML_TEST.r
Analyse_project_new_GENO_DUMP.AML_TEST_SYON.r		Analyse_project_new_GENO_DUMP.AML_TEST_SYON.r
Analyse_project_new_GENO_DUMP.r		Analyse_project_new_GENO_DUMP.r
Analyse_project_new_GENO_DUMP_2015.r		Analyse_project_new_GENO_DUMP_2015.r
Analyse_project_new_GENO_DUMP_2015_AML.r		Analyse_project_new_GENO_DUMP_2015_AML.r
Analyse_project_new_GENO_DUMP_RUNNER.r		Analyse_project_new_GENO_DUMP_RUNNER.r
Analyse_project_new_NMD.r		Analyse_project_new_NMD.r
Analyse_project_new_NMD_Paul.r		Analyse_project_new_NMD_Paul.r
Analyse_project_new_NMD_Paul_controls.r		Analyse_project_new_NMD_Paul_controls.r
Analyse_project_new_NMD_Paul_geno.dump.r		Analyse_project_new_NMD_Paul_geno.dump.r
Analyse_project_new_Project_RUNNER.r		Analyse_project_new_Project_RUNNER.r
Annotate.logistic.r		Annotate.logistic.r
Annotate_bim_file.r		Annotate_bim_file.r
Annotate_sequence_run.r		Annotate_sequence_run.r
Annotate_sequence_run_2015.r		Annotate_sequence_run_2015.r
Annotate_sequence_run_Aug_2014.r		Annotate_sequence_run_Aug_2014.r
Annotate_sequence_run_Aug_2014_AOGC.r		Annotate_sequence_run_Aug_2014_AOGC.r
Annotate_sequence_run_Aug_2014_BONE.r		Annotate_sequence_run_Aug_2014_BONE.r
Annotate_sequence_run_Aug_2014_BONE_MURCURY.r		Annotate_sequence_run_Aug_2014_BONE_MURCURY.r
Annotate_sequence_run_Aug_2015.r		Annotate_sequence_run_Aug_2015.r
Annotate_sequence_run_RUNNER.r		Annotate_sequence_run_RUNNER.r
Apply inheritance QC_MUILT_NEW.r		Apply inheritance QC_MUILT_NEW.r
Apply inheritance QC_MUILT_NEW_PCA.r		Apply inheritance QC_MUILT_NEW_PCA.r
Apply inheritance QC_MUILT_NEW_PCA_FAST.r		Apply inheritance QC_MUILT_NEW_PCA_FAST.r
Apply inheritance QC_MUILT_NEW_PCA_ULTRA.r		Apply inheritance QC_MUILT_NEW_PCA_ULTRA.r
Apply inheritance QC_MUILT_NEW_PCA_ULTRA.v1.r		Apply inheritance QC_MUILT_NEW_PCA_ULTRA.v1.r
ApplyinheritanceQC_MUILT_NEW.r		ApplyinheritanceQC_MUILT_NEW.r
BEM2NT~M.TXT		BEM2NT~M.TXT
BIIJ8S~2.TXT		BIIJ8S~2.TXT
BY0VJ2~7.TXT		BY0VJ2~7.TXT
Best.base.quality.using.Rsamtools.r		Best.base.quality.using.Rsamtools.r
BreakDancer_analsyis.r		BreakDancer_analsyis.r
Burden.ALL.coding.somatic.with.Indels.noBenign.new.RECOVERY.withGQ.noMissing.FINALtest.Wgts.txt		Burden.ALL.coding.somatic.with.Indels.noBenign.new.RECOVERY.withGQ.noMissing.FINALtest.Wgts.txt
Burden.coding.0.001.all.geno.all.filters.txt		Burden.coding.0.001.all.geno.all.filters.txt

achalneupane/rcodes

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