Major update: EM for sequence now support background class Important code…
1bfc0a93ba65
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Authored by rgroux on Aug 19 2019, 14:48.

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Major update: EM for sequence now support background class Important code refactor and EM broken into 3 exec Code to extend short models given data Peak analysis started

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rgroux

Aug 19 2019, 14:48

Pushed

rgroux

Aug 19 2019, 14:53

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R8820:c65a488e1038: Sequence layer fully supported Sequence matrices construction and EM motif…

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rgroux committed R8820:1bfc0a93ba65: Major update: EM for sequence now support background class Important code… (authored by rgroux).Aug 19 2019, 14:48

Changes (152)

		Path
D		res/A.png.save
D		res/C.png.save
D		res/G.png.save
D		res/T.png.save
D		scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif_chr1.R
D		scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif_chr1.sh
M		scripts/10xgenomics_PBMC_5k/analysis_peaks.sh
M		scripts/10xgenomics_PBMC_5k/process_data.sh
M		scripts/10xgenomics_PBMC_5k/run_all.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.sh
M		scripts/10xgenomics_PBMC_5k_classification_1/classification_myc_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_1/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
M		scripts/10xgenomics_PBMC_5k_classification_3/classification_ctcf_motif.sh
P		scripts/10xgenomics_PBMC_5k_classification_3/classification_sp1_motif.sh Copied to scripts/10xgenomics_PBMC_5k_classification_4/classification_sp1_motif.sh
M		scripts/10xgenomics_PBMC_5k_classification_4/classification_ctcf_motif.sh
P		scripts/10xgenomics_PBMC_5k_classification_4/classification_sp1_motif.R Copied from scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.R
P		scripts/10xgenomics_PBMC_5k_classification_4/classification_sp1_motif.sh Copied from scripts/10xgenomics_PBMC_5k_classification_3/classification_sp1_motif.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks/
A		scripts/10xgenomics_PBMC_5k_peaks/analysis_peaks.sh
A		scripts/10xgenomics_PBMC_5k_peaks/analysis_peaks_sampled.sh
A		scripts/10xgenomics_PBMC_5k_peaks_classification_1/analysis_test_sampled.R
P		scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.R Deleted after being copied to multiple locations: scripts/10xgenomics_PBMC_5k_classification_4/classification_sp1_motif.R scripts/10xgenomics_PBMC_5k_peaks_classification_7/analysis_test.R
D		scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.sh
A		scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks_sampled.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks_classification_2/
A		scripts/10xgenomics_PBMC_5k_peaks_classification_2/analysis_test_sampled.R
A		scripts/10xgenomics_PBMC_5k_peaks_classification_2/classification_peaks_sampled.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks_classification_3/
A		scripts/10xgenomics_PBMC_5k_peaks_classification_3/analysis_test_sampled.R
A		scripts/10xgenomics_PBMC_5k_peaks_classification_3/classification_peaks_sampled.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks_classification_4/
A		scripts/10xgenomics_PBMC_5k_peaks_classification_4/analysis_test_sampled.R
A		scripts/10xgenomics_PBMC_5k_peaks_classification_4/classification_peaks_sampled.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks_classification_5/
A		scripts/10xgenomics_PBMC_5k_peaks_classification_5/analysis_test_sampled.R
A		scripts/10xgenomics_PBMC_5k_peaks_classification_5/classification_peaks_sampled.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks_classification_6/
A		scripts/10xgenomics_PBMC_5k_peaks_classification_6/analysis_test_sampled.R
A		scripts/10xgenomics_PBMC_5k_peaks_classification_6/classification_peaks_sampled.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks_classification_7/
V		scripts/{10xgenomics_PBMC_5k_peaks_classification_7/analysis_test.R ← 10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.R}
A		scripts/10xgenomics_PBMC_5k_peaks_classification_7/classification_peaks.sh
M		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
M		scripts/functions.R
A	(dir)	scripts/genomes/
A		scripts/genomes/hg19.sh
A		scripts/install_libraries/install_libUnitTest++.sh
A		scripts/install_libraries/install_libboost.sh
M		scripts/install_libraries/run_all.sh
A		scripts/install_programs/install_bedtools.sh
D		scripts/install_programs/install_deeptools.sh
M		scripts/install_programs/run_all.sh
A	(dir)	scripts/pwm/
A		scripts/pwm/reformat_jaspar_2018.sh
A		scripts/pwm/reformat_jaspar_2018_clustering.sh
A	(dir)	scripts/pwm_tools/
A		scripts/pwm_tools/extract_transfac_pwm.py
M		scripts/run_all.sh
A		scripts/test.R
A		scripts/test/analysis_test_sampled.R
D		scripts/test/test.sh
A		scripts/test/test_1kb.sh
A		scripts/test/test_1kb_pwms.sh
A		scripts/test/test_1kb_sampled.sh
A		scripts/test/test_1kb_sampled_pwms.sh
A		scripts/test/test_2kb.sh
A		scripts/test/test_2kb_sampled.sh
A	(dir)	scripts/test_2/
A		scripts/test_2/analysis_test_2_sampled.R
A		scripts/test_2/test_1kb_sampled.sh
A		scripts/test_2/test_2kb_sampled.sh
A		scripts/test_dendrogram.R
P		src/Applications/ChIPPartitioningApplication.cpp Copied to multiple locations: src/Applications/EMJointApplication.cpp src/Applications/EMReadApplication.cpp
P		src/Applications/ChIPPartitioningApplication.hpp Copied to multiple locations: src/Applications/EMJointApplication.hpp src/Applications/EMReadApplication.hpp src/Applications/EMSequenceApplication.hpp
M		src/Applications/CorrelationMatrixCreatorApplication.cpp
P		src/Applications/EMJointApplication.cpp Copied from src/Applications/ChIPPartitioningApplication.cpp
P		src/Applications/EMJointApplication.hpp Copied from src/Applications/ChIPPartitioningApplication.hpp
P		src/Applications/EMReadApplication.cpp Copied from src/Applications/ChIPPartitioningApplication.cpp
P		src/Applications/EMReadApplication.hpp Copied from src/Applications/ChIPPartitioningApplication.hpp
A		src/Applications/EMSequenceApplication.cpp
P		src/Applications/EMSequenceApplication.hpp Copied from src/Applications/ChIPPartitioningApplication.hpp
M		src/Applications/ProbToModelApplication.cpp
A		src/Applications/ReadModelExtenderApplication.cpp
A		src/Applications/ReadModelExtenderApplication.hpp
A		src/Applications/SequenceModelExtenderApplication.cpp
A		src/Applications/SequenceModelExtenderApplication.hpp
M		src/CMakeLists.txt
D		src/Clustering.old
D		src/Clustering.old/ClusteringEngine.cpp
D		src/Clustering.old/ClusteringEngine.hpp
D		src/Clustering.old/EMEngine.cpp
D		src/Clustering.old/EMEngine.hpp
D		src/Clustering.old/ReferenceComputer.cpp
D		src/Clustering.old/ReferenceComputer.hpp
D		src/Clustering.old/typedef.hpp
M		src/Clustering/DataLayer.cpp
M		src/Clustering/DataLayer.hpp
A		src/Clustering/EMBase.cpp
A		src/Clustering/EMBase.hpp
D		src/Clustering/EMEngine.cpp
D		src/Clustering/EMEngine.cpp.save
D		src/Clustering/EMEngine.hpp
D		src/Clustering/EMEngine.hpp.save
A		src/Clustering/EMJoint.cpp
A		src/Clustering/EMJoint.hpp
A		src/Clustering/EMRead.cpp
A		src/Clustering/EMRead.hpp
A		src/Clustering/EMSequence.cpp
A		src/Clustering/EMSequence.hpp
M		src/Clustering/ModelComputer.cpp
M		src/Clustering/ModelComputer.hpp
M		src/Clustering/ReadLayer.cpp
M		src/Clustering/ReadLayer.hpp
M		src/Clustering/ReadModelComputer.cpp
M		src/Clustering/ReadModelComputer.hpp
M		src/Clustering/SequenceLayer.cpp
M		src/Clustering/SequenceLayer.hpp
M		src/Clustering/SequenceModelComputer.cpp
M		src/Clustering/SequenceModelComputer.hpp
M		src/GenomicTools/CorrelationMatrixCreator.cpp
M		src/GenomicTools/CorrelationMatrixCreator.hpp
M		src/GenomicTools/MatrixCreator.cpp
M		src/GenomicTools/MatrixCreator.hpp
M		src/GenomicTools/ReadMatrixCreator.hpp
M		src/GenomicTools/SequenceMatrixCreator.cpp
M		src/GenomicTools/SequenceMatrixCreator.hpp
M		src/Matrix/Matrix.hpp
M		src/Matrix/Matrix2D.hpp
M		src/Matrix/Matrix3D.hpp
M		src/Matrix/Matrix4D.hpp
M		src/Random/Random.cpp
M		src/Random/Random.hpp
M		src/Unittests/unittests_genomictools.cpp
M		src/Unittests/unittests_matrix.cpp
M		src/Utility/dna_utility.cpp
M		src/Utility/dna_utility.hpp
M		src/main_cormat.cpp
M		src/main_em.cpp
M		src/main_em2.cpp