Amberkar_Scripts

This repository consists of all scripts created by Sandeep Amberkar.

Name		Name	Last commit message	Last commit date
Latest commit History 342 Commits
.DS_Store		.DS_Store
.gitattributes		.gitattributes
Berchtold_diffcoexp_analysis.R		Berchtold_diffcoexp_analysis.R
Berchtold_diffcoexp_analysis.sh		Berchtold_diffcoexp_analysis.sh
Berchtold_diffcoexp_functional_analysis.R		Berchtold_diffcoexp_functional_analysis.R
DiffCorr_Genes_Functions.R		DiffCorr_Genes_Functions.R
Emory_Analysis.R		Emory_Analysis.R
IPAH_DEG_Analysis.Rmd		IPAH_DEG_Analysis.Rmd
IPAH_DEG_Analysis.html		IPAH_DEG_Analysis.html
IPAH_DEG_Analysis2.Rmd		IPAH_DEG_Analysis2.Rmd
IPAH_DEG_Analysis2.html		IPAH_DEG_Analysis2.html
LICENSE		LICENSE
MSBB_Pathprint_Geneset_Analysis.R		MSBB_Pathprint_Geneset_Analysis.R
MSBB_plague_subsets.R		MSBB_plague_subsets.R
MSMM_PathPrint_SigAnalysis.R		MSMM_PathPrint_SigAnalysis.R
OA_AnalyseRewire.R		OA_AnalyseRewire.R
README.md		README.md
RSynapse_iceberg.R		RSynapse_iceberg.R
STAR_Align.sh		STAR_Align.sh
STAR_GenomeIndex.sh		STAR_GenomeIndex.sh
ScalaTutorial.scala		ScalaTutorial.scala
TDP_Align.R		TDP_Align.R
TDP_Align_Submit.sh		TDP_Align_Submit.sh
Test.Rmd		Test.Rmd
Test.html		Test.html
Test.pdf		Test.pdf
als_DCN_meta_analysis.R		als_DCN_meta_analysis.R
als_dcn_analysis_fcx_sALS.R		als_dcn_analysis_fcx_sALS.R
als_dcn_analysis_iceberg.sh		als_dcn_analysis_iceberg.sh
als_dcn_analysis_sALS_neurons_iceberg.R		als_dcn_analysis_sALS_neurons_iceberg.R
als_dcn_analysis_sALS_neurons_iceberg.sh		als_dcn_analysis_sALS_neurons_iceberg.sh
als_dcn_fcx_C9Orf72_analysis_iceberg.R		als_dcn_fcx_C9Orf72_analysis_iceberg.R
als_dcn_rewire_fcx_sALS.R		als_dcn_rewire_fcx_sALS.R
amp_AD_reseq_DCN_meta_analysis2.R		amp_AD_reseq_DCN_meta_analysis2.R
amp_ad_reseq_DCN_meta_analysis.R		amp_ad_reseq_DCN_meta_analysis.R
cocor_parallel_test.R		cocor_parallel_test.R
cocor_parallel_working.R		cocor_parallel_working.R
d_tutorial		d_tutorial
d_tutorial.d		d_tutorial.d
d_tutorial.o		d_tutorial.o
dcn_rewire_threshold_optimise.R		dcn_rewire_threshold_optimise.R
dcn_rewire_threshold_optimise.sh		dcn_rewire_threshold_optimise.sh
diffcoexp.R		diffcoexp.R
earlyAD_TFbridgedDCL_downstream_GO_analysis.R		earlyAD_TFbridgedDCL_downstream_GO_analysis.R
earlyAD_TFbridgedDCL_downstream_GO_analysis.sh		earlyAD_TFbridgedDCL_downstream_GO_analysis.sh
git-credential-osxkeychain		git-credential-osxkeychain
gtk-osx-build-setup.sh		gtk-osx-build-setup.sh
hs_ppi_preprocess.R		hs_ppi_preprocess.R
iRef14_Human_PPI.R		iRef14_Human_PPI.R
ipah_DCN_analysis.R		ipah_DCN_analysis.R
ipah_DCN_functional_analysis.R		ipah_DCN_functional_analysis.R
ipah_covariate_preprocess.R		ipah_covariate_preprocess.R
ipah_pilot_150bp_DCN_analysis.R		ipah_pilot_150bp_DCN_analysis.R
ipah_pilot_150bp_DCN_analysis.sh		ipah_pilot_150bp_DCN_analysis.sh
ipah_pilot_DCN_analysis.R		ipah_pilot_DCN_analysis.R
ipah_pilot_DCN_analysis.sh		ipah_pilot_DCN_analysis.sh
ipah_preprocess.R		ipah_preprocess.R
lateAD_TFbridgedDCL_downstream_GO_analysis.R		lateAD_TFbridgedDCL_downstream_GO_analysis.R
lateAD_TFbridgedDCL_downstream_GO_analysis.sh		lateAD_TFbridgedDCL_downstream_GO_analysis.sh
mayo_Aging_DiffPathway_analysis.R		mayo_Aging_DiffPathway_analysis.R
mayo_cer_DCL_analysis.R		mayo_cer_DCL_analysis.R
mayo_cer_DCL_analysis.sh		mayo_cer_DCL_analysis.sh
mayo_cer_DiffCoexp_DCL_analysis.R		mayo_cer_DiffCoexp_DCL_analysis.R
mayo_cer_DiffCoexp_DCL_analysis.sh		mayo_cer_DiffCoexp_DCL_analysis.sh
mayo_cer_dCG_PermutationTest.R		mayo_cer_dCG_PermutationTest.R
mayo_dCG_PermutationTest.R		mayo_dCG_PermutationTest.R
mayo_reseq_CER_DCN_analysis.R		mayo_reseq_CER_DCN_analysis.R
mayo_reseq_CER_DCN_analysis.sh		mayo_reseq_CER_DCN_analysis.sh
mayo_reseq_DCN_analysis.R		mayo_reseq_DCN_analysis.R
mayo_reseq_DCN_analysis.sh		mayo_reseq_DCN_analysis.sh
mayo_reseq_TCX_DCN_analysis.R		mayo_reseq_TCX_DCN_analysis.R
mayo_reseq_TCX_DCN_analysis.sh		mayo_reseq_TCX_DCN_analysis.sh
mayo_tcx_DCL_analysis.R		mayo_tcx_DCL_analysis.R
mayo_tcx_DCL_analysis.sh		mayo_tcx_DCL_analysis.sh
mayo_tcx_DiffCoexp_DCL_analysis.R		mayo_tcx_DiffCoexp_DCL_analysis.R
mayo_tcx_DiffCoexp_DCL_analysis.sh		mayo_tcx_DiffCoexp_DCL_analysis.sh
mayo_tcx_dCG_PermutationTest.R		mayo_tcx_dCG_PermutationTest.R
metaAD_DCG_DCL_VariantComparison.R		metaAD_DCG_DCL_VariantComparison.R
msbb_CDR_early_diffcoexp.R		msbb_CDR_early_diffcoexp.R
msbb_CDR_early_diffcoexp.sh		msbb_CDR_early_diffcoexp.sh
msbb_CDR_early_diffcoexp_functional_analysis.R		msbb_CDR_early_diffcoexp_functional_analysis.R
msbb_DCN_ResistomeAnalysis.R		msbb_DCN_ResistomeAnalysis.R
msbb_array_DEG_analysis.R		msbb_array_DEG_analysis.R
msbb_array_diffcoexp.R		msbb_array_diffcoexp.R
msbb_array_diffcoexp.sh		msbb_array_diffcoexp.sh
msbb_array_diffcoexp2.R		msbb_array_diffcoexp2.R
msbb_array_diffcoexp2.sh		msbb_array_diffcoexp2.sh
msbb_array_diffcoexp2_TDD_analysis.R		msbb_array_diffcoexp2_TDD_analysis.R
msbb_array_diffcoexp2_TDD_analysis.sh		msbb_array_diffcoexp2_TDD_analysis.sh
msbb_array_diffcoexp2_TED_TDD_analysis.R		msbb_array_diffcoexp2_TED_TDD_analysis.R
msbb_array_diffcoexp2_TED_analysis.R		msbb_array_diffcoexp2_TED_analysis.R
msbb_array_diffcoexp2_TED_analysis.sh		msbb_array_diffcoexp2_TED_analysis.sh
msbb_array_diffcoexp2_functional_analysis.R		msbb_array_diffcoexp2_functional_analysis.R
msbb_array_diffcoexp3.R		msbb_array_diffcoexp3.R
msbb_array_diffcoexp4.R		msbb_array_diffcoexp4.R
msbb_array_diffcoexp4.sh		msbb_array_diffcoexp4.sh
msbb_array_diffcoexp4_TED_analysis.R		msbb_array_diffcoexp4_TED_analysis.R
msbb_array_diffcoexp4_TED_analysis.sh		msbb_array_diffcoexp4_TED_analysis.sh
msbb_array_diffcoexp4_functional_analysis.R		msbb_array_diffcoexp4_functional_analysis.R
msbb_array_diffcoexp5.R		msbb_array_diffcoexp5.R

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