Diffusion scATAC-seq c65a488e1038

Sequence layer fully supported Sequence matrices construction and EM motif…
c65a488e1038
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Authored by rgroux on Jul 25 2019, 09:16.

Description

Sequence layer fully supported Sequence matrices construction and EM motif search added

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Committed

rgroux

Jul 25 2019, 09:17

Pushed

rgroux

Jul 25 2019, 17:54

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R8820:f158c081ec79: Support for sequence layer under dev

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rgroux committed R8820:c65a488e1038: Sequence layer fully supported Sequence matrices construction and EM motif… (authored by rgroux).Jul 25 2019, 09:17

Changes (105)

		Path
A	(dir)	res/
A		res/A.png
A		res/A.png.save
A		res/C.png
A		res/C.png.save
A		res/G.png
A		res/G.png.save
A		res/T.png
A		res/T.png.save
M		scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif.sh
M		scripts/10xgenomics_PBMC_5k/analysis_ebf1_motif.sh
M		scripts/10xgenomics_PBMC_5k/analysis_myc_motif.sh
A		scripts/10xgenomics_PBMC_5k/analysis_peaks.sh
M		scripts/10xgenomics_PBMC_5k/analysis_sp1_motif.sh
M		scripts/10xgenomics_PBMC_5k/split_by_size.sh
D		scripts/10xgenomics_PBMC_5k_classification_1.save
D		scripts/10xgenomics_PBMC_5k_classification_1.save/classification_ctcf_motif.R
D		scripts/10xgenomics_PBMC_5k_classification_1.save/classification_ctcf_motif.sh
D		scripts/10xgenomics_PBMC_5k_classification_1.save/classification_ebf1_motif.R
D		scripts/10xgenomics_PBMC_5k_classification_1.save/classification_ebf1_motif.sh
D		scripts/10xgenomics_PBMC_5k_classification_1.save/classification_myc_motif.R
D		scripts/10xgenomics_PBMC_5k_classification_1.save/classification_myc_motif.sh
D		scripts/10xgenomics_PBMC_5k_classification_1.save/classification_sp1_motif.R
D		scripts/10xgenomics_PBMC_5k_classification_1.save/classification_sp1_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_ctcf_motif.R
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_ctcf_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_ebf1_motif.R
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_ebf1_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_myc_motif.R
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_myc_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_sp1_motif.R
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_sp1_motif.sh
D		scripts/10xgenomics_PBMC_5k_classification_2.save
D		scripts/10xgenomics_PBMC_5k_classification_2.save/classification_ctcf_motif.R
D		scripts/10xgenomics_PBMC_5k_classification_2.save/classification_ctcf_motif.sh
D		scripts/10xgenomics_PBMC_5k_classification_2.save/classification_ebf1_motif.R
D		scripts/10xgenomics_PBMC_5k_classification_2.save/classification_ebf1_motif.sh
D		scripts/10xgenomics_PBMC_5k_classification_2.save/classification_myc_motif.R
D		scripts/10xgenomics_PBMC_5k_classification_2.save/classification_myc_motif.sh
D		scripts/10xgenomics_PBMC_5k_classification_2.save/classification_sp1_motif.R
D		scripts/10xgenomics_PBMC_5k_classification_2.save/classification_sp1_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_2/classification_ctcf_motif.R
M		scripts/10xgenomics_PBMC_5k_classification_2/classification_ctcf_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_2/classification_ebf1_motif.R
M		scripts/10xgenomics_PBMC_5k_classification_2/classification_ebf1_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_2/classification_myc_motif.R
M		scripts/10xgenomics_PBMC_5k_classification_2/classification_myc_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_2/classification_sp1_motif.R
M		scripts/10xgenomics_PBMC_5k_classification_2/classification_sp1_motif.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_classification_3/
A		scripts/10xgenomics_PBMC_5k_classification_3/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_3/classification_ctcf_motif.sh
A		scripts/10xgenomics_PBMC_5k_classification_3/classification_sp1_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_3/classification_sp1_motif.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_classification_4/
A		scripts/10xgenomics_PBMC_5k_classification_4/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_classification_4/classification_ctcf_motif.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks_classification_1/
A		scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.R
A		scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.sh
M		scripts/functions.R
A	(dir)	scripts/test/
A		scripts/test/test.sh
A		scripts/toy_data/generate_matrix_data_sequence.R
M		src/Applications/ChIPPartitioningApplication.cpp
M		src/Applications/CorrelationMatrixCreatorApplication.cpp
M		src/Applications/CorrelationMatrixCreatorApplication.hpp
D		src/Applications/CorrelationMatrixCreatorApplicationParallel.cpp
V		src/Applications/{CorrelationMatrixCreatorApplicationParallel.hpp → SequenceMatrixCreatorApplication.hpp}
M		src/Applications/ProbToModelApplication.cpp
A		src/Applications/SequenceMatrixCreatorApplication.cpp
V		src/Applications/{SequenceMatrixCreatorApplication.hpp ← CorrelationMatrixCreatorApplicationParallel.hpp}
D		src/Clustering/DataLayer.cpp.save
D		src/Clustering/DataLayer.hpp.save
P		src/Clustering/EMEngine.cpp Copied to src/Clustering/EMEngine.cpp.save
P		src/Clustering/EMEngine.cpp.save Copied from src/Clustering/EMEngine.cpp
P		src/Clustering/EMEngine.hpp Copied to src/Clustering/EMEngine.hpp.save
P		src/Clustering/EMEngine.hpp.save Copied from src/Clustering/EMEngine.hpp
M		src/Clustering/ModelComputer.hpp
M		src/Clustering/ReadLayer.cpp
M		src/Clustering/SequenceLayer.cpp
M		src/Clustering/SequenceLayer.hpp
M		src/GenomicTools/CorrelationMatrixCreator.cpp
M		src/GenomicTools/CorrelationMatrixCreator.hpp
D		src/GenomicTools/CorrelationMatrixCreatorParallel.cpp
D		src/GenomicTools/CorrelationMatrixCreatorParallel.hpp
P		src/GenomicTools/MatrixCreator.cpp Copied to src/GenomicTools/ReadMatrixCreator.cpp
P		src/GenomicTools/MatrixCreator.hpp Copied to src/GenomicTools/ReadMatrixCreator.hpp
D		src/GenomicTools/MatrixCreatorParallel.cpp
D		src/GenomicTools/MatrixCreatorParallel.hpp
P		src/GenomicTools/ReadMatrixCreator.cpp Copied from src/GenomicTools/MatrixCreator.cpp
P		src/GenomicTools/ReadMatrixCreator.hpp Copied from src/GenomicTools/MatrixCreator.hpp
A		src/GenomicTools/SequenceMatrixCreator.cpp
A		src/GenomicTools/SequenceMatrixCreator.hpp
A		src/Random/BetaDistribution.hpp
M		src/Unittests/unittests_genomictools.cpp
D		src/Utility/Utility.cpp
D		src/Utility/Utility.hpp
D		src/Utility/Vector_utility.hpp
M		src/Utility/dna_utility.cpp
M		src/Utility/dna_utility.hpp
M		src/Utility/matrices.cpp
M		src/Utility/matrices.hpp
M		src/main_cormat.cpp
M		src/main_em.cpp