1)ATAC-seq data subsets created for open chromatin and nucleosomes. 2)Code to…
faf6f1d50a68
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Authored by rgroux on Jun 18 2019, 08:55.

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1)ATAC-seq data subsets created for open chromatin and nucleosomes. 2)Code to build correlation matrices.

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rgroux

Jul 3 2019, 16:17

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rgroux

Jul 3 2019, 16:27

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R8820:5ff7043d02d8: AIC computation added to ChIPPartitioning impl

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rgroux committed R8820:faf6f1d50a68: 1)ATAC-seq data subsets created for open chromatin and nucleosomes. 2)Code to… (authored by rgroux).Jul 3 2019, 16:17

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		Path
M		.gitignore
M		CMakeLists.txt
A		build.sh
A	(dir)	scripts/10xgenomics_PBMC_5k/
A		scripts/10xgenomics_PBMC_5k/.10xgenomics.sh.swp
A	(dir)	scripts/10xgenomics_PBMC_5k/.idea/
A		scripts/10xgenomics_PBMC_5k/.idea/encodings.xml
A	(dir)	scripts/10xgenomics_PBMC_5k/.idea/libraries/
A		scripts/10xgenomics_PBMC_5k/.idea/libraries/R_User_Library.xml
A		scripts/10xgenomics_PBMC_5k/.idea/misc.xml
A		scripts/10xgenomics_PBMC_5k/.idea/modules.xml
A		scripts/10xgenomics_PBMC_5k/.idea/scripts.iml
A		scripts/10xgenomics_PBMC_5k/.idea/workspace.xml
A		scripts/10xgenomics_PBMC_5k/analyse_fragment_lengths.R
A		scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif.sh
A		scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif_chr1.R
A		scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif_chr1.sh
A		scripts/10xgenomics_PBMC_5k/analysis_ebf1_motif.R
A		scripts/10xgenomics_PBMC_5k/analysis_ebf1_motif.sh
A		scripts/10xgenomics_PBMC_5k/analysis_myc_motif.R
A		scripts/10xgenomics_PBMC_5k/analysis_myc_motif.sh
A		scripts/10xgenomics_PBMC_5k/analysis_sp1_motif.R
A		scripts/10xgenomics_PBMC_5k/analysis_sp1_motif.sh
A		scripts/10xgenomics_PBMC_5k/process_data.sh
A		scripts/10xgenomics_PBMC_5k/run_all.sh
A		scripts/10xgenomics_PBMC_5k/split_by_size.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_classification_1/
A		scripts/10xgenomics_PBMC_5k_classification_1/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_1/classification_ctcf_motif.sh
A		scripts/10xgenomics_PBMC_5k_classification_1/classification_ebf1_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_1/classification_ebf1_motif.sh
A		scripts/10xgenomics_PBMC_5k_classification_1/classification_myc_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_1/classification_myc_motif.sh
A		scripts/10xgenomics_PBMC_5k_classification_1/classification_sp1_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_1/classification_sp1_motif.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_classification_2/
A		scripts/10xgenomics_PBMC_5k_classification_2/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_2/classification_ctcf_motif.sh
A		scripts/10xgenomics_PBMC_5k_classification_2/classification_ebf1_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_2/classification_ebf1_motif.sh
A		scripts/10xgenomics_PBMC_5k_classification_2/classification_myc_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_2/classification_myc_motif.sh
A		scripts/10xgenomics_PBMC_5k_classification_2/classification_sp1_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_2/classification_sp1_motif.sh
A	(dir)	scripts/bam_tools/
A	(dir)	scripts/bam_tools/.idea/
A		scripts/bam_tools/.idea/bam_tools.iml
A		scripts/bam_tools/.idea/encodings.xml
A	(dir)	scripts/bam_tools/.idea/libraries/
A		scripts/bam_tools/.idea/libraries/R_User_Library.xml
A		scripts/bam_tools/.idea/misc.xml
A		scripts/bam_tools/.idea/modules.xml
A		scripts/bam_tools/.idea/workspace.xml
A		scripts/bam_tools/filter_bam.py
A		scripts/bam_tools/head_bam.py
A		scripts/bam_tools/split_bam.py
A		scripts/bam_tools/split_by_length.py
A		scripts/bam_tools/split_in_two.py
A		scripts/bulk_sequencing/analysis_cluster_ctcf_dnase_k562.R
M		scripts/bulk_sequencing/analysis_cluster_ctcf_mnase_k562.R
M		scripts/bulk_sequencing/cluster_ctcf_dnase_k562.sh
M		scripts/bulk_sequencing/cluster_ctcf_mnase_k562.sh
A		scripts/bulk_sequencing/functions.R
M		scripts/bulk_sequencing/prepare_data.R
A		scripts/functions.R
A	(dir)	scripts/install_libraries/
A		scripts/install_libraries/install_libSeqAn.sh
A		scripts/install_libraries/run_all.sh
A	(dir)	scripts/install_programs/
A		scripts/install_programs/install_deeptools.sh
A		scripts/install_programs/run_all.sh
D		scripts/plot_references.R
M		scripts/run_all.sh
D		scripts/simulate_chipseq_data
D		scripts/simulate_chipseq_data/run_all.sh
V		scripts/{simulate_chipseq_data/simulate_data_chipseq.R → toy_data/generate_matrix_data_chipseq.R}
A	(dir)	scripts/toy_data/
A		scripts/toy_data/generate_bam_file.py
A		scripts/toy_data/generate_bed_file.py
V		scripts/{toy_data/generate_matrix_data_chipseq.R ← simulate_chipseq_data/simulate_data_chipseq.R}
A		scripts/toy_data/run_all.sh
A		src/Applications/CorrelationMatrixCreatorApplication.cpp
A		src/Applications/CorrelationMatrixCreatorApplication.hpp
A		src/Applications/CorrelationMatrixCreatorApplicationParallel.cpp
A		src/Applications/CorrelationMatrixCreatorApplicationParallel.hpp
M		src/CMakeLists.txt
M		src/Clustering/EMEngine.cpp
M		src/Clustering/EMEngine.hpp
M		src/Clustering/ReferenceComputer.cpp
M		src/Clustering/typedef.hpp
A	(dir)	src/GenomicTools/
A		src/GenomicTools/CellMatrixCreator.cpp
A		src/GenomicTools/CellMatrixCreator.hpp
A		src/GenomicTools/CorrelationMatrixCreator.cpp
A		src/GenomicTools/CorrelationMatrixCreator.hpp
A		src/GenomicTools/CorrelationMatrixCreatorParallel.cpp
A		src/GenomicTools/CorrelationMatrixCreatorParallel.hpp
A		src/GenomicTools/GenomeRegion.cpp
A		src/GenomicTools/GenomeRegion.hpp
A		src/GenomicTools/MatrixCreator.cpp
A		src/GenomicTools/MatrixCreator.hpp
A		src/GenomicTools/MatrixCreatorParallel.cpp
A		src/GenomicTools/MatrixCreatorParallel.hpp
A		src/GenomicTools/typedef.hpp
M		src/Matrix/Matrix.hpp
M		src/Matrix/Matrix2D.hpp
M		src/Matrix/Matrix3D.hpp
M		src/Matrix/Matrix4D.hpp
D		src/Matrix_old
D		src/Matrix_old/Matrix.hpp
D		src/Matrix_old/Matrix2D.hpp
D		src/Matrix_old/Matrix3D.hpp
D		src/Matrix_old/Matrix4D.hpp
M		src/Parallel/ThreadPool.cpp
M		src/Statistics/Statistics.cpp
A		src/Unittests/unittests_genomictools.cpp
M		src/Unittests/unittests_matrix.cpp
D		src/main.cpp
A		src/main_cormat.cpp
A		src/main_em.cpp
A		src/main_seqan.cpp