Homec4science
Diffusion scATAC-seq 1bfc0a93ba65

Major update: EM for sequence now support background class Important code…
1bfc0a93ba65
Actions

Authored by rgroux on Aug 19 2019, 14:48.

Description

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

Details

Committed
rgrouxAug 19 2019, 14:48
Pushed
rgrouxAug 19 2019, 14:53
Parents
R8820:c65a488e1038: Sequence layer fully supported Sequence matrices construction and EM motif…
Branches
Unknown
Tags
Unknown

Changes (152)
Show All Changes

Very Large Commit

This commit is very large. Load each file individually.
Path
Dres/A.png.save
Dres/C.png.save
Dres/G.png.save
Dres/T.png.save
Dscripts/10xgenomics_PBMC_5k/analysis_ctcf_motif_chr1.R
Dscripts/10xgenomics_PBMC_5k/analysis_ctcf_motif_chr1.sh
Mscripts/10xgenomics_PBMC_5k/analysis_peaks.sh
Mscripts/10xgenomics_PBMC_5k/process_data.sh
Mscripts/10xgenomics_PBMC_5k/run_all.sh
Mscripts/10xgenomics_PBMC_5k_classification_1/classification_ctcf_motif.R
Mscripts/10xgenomics_PBMC_5k_classification_1/classification_ctcf_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_1/classification_ebf1_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_1/classification_myc_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_1/classification_sp1_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_2/classification_ctcf_motif.R
Mscripts/10xgenomics_PBMC_5k_classification_2/classification_ctcf_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_2/classification_ebf1_motif.R
Mscripts/10xgenomics_PBMC_5k_classification_2/classification_ebf1_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_2/classification_myc_motif.R
Mscripts/10xgenomics_PBMC_5k_classification_2/classification_myc_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_2/classification_sp1_motif.R
Mscripts/10xgenomics_PBMC_5k_classification_2/classification_sp1_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_3/classification_ctcf_motif.sh
Pscripts/10xgenomics_PBMC_5k_classification_3/classification_sp1_motif.sh
Copied to scripts/10xgenomics_PBMC_5k_classification_4/classification_sp1_motif.sh
Mscripts/10xgenomics_PBMC_5k_classification_4/classification_ctcf_motif.sh
Pscripts/10xgenomics_PBMC_5k_classification_4/classification_sp1_motif.R
Copied from scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.R
Pscripts/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/
Ascripts/10xgenomics_PBMC_5k_peaks/analysis_peaks.sh
Ascripts/10xgenomics_PBMC_5k_peaks/analysis_peaks_sampled.sh
Ascripts/10xgenomics_PBMC_5k_peaks_classification_1/analysis_test_sampled.R
Pscripts/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
Dscripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.sh
Ascripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks_sampled.sh
A(dir)scripts/10xgenomics_PBMC_5k_peaks_classification_2/
Ascripts/10xgenomics_PBMC_5k_peaks_classification_2/analysis_test_sampled.R
Ascripts/10xgenomics_PBMC_5k_peaks_classification_2/classification_peaks_sampled.sh
A(dir)scripts/10xgenomics_PBMC_5k_peaks_classification_3/
Ascripts/10xgenomics_PBMC_5k_peaks_classification_3/analysis_test_sampled.R
Ascripts/10xgenomics_PBMC_5k_peaks_classification_3/classification_peaks_sampled.sh
A(dir)scripts/10xgenomics_PBMC_5k_peaks_classification_4/
Ascripts/10xgenomics_PBMC_5k_peaks_classification_4/analysis_test_sampled.R
Ascripts/10xgenomics_PBMC_5k_peaks_classification_4/classification_peaks_sampled.sh
A(dir)scripts/10xgenomics_PBMC_5k_peaks_classification_5/
Ascripts/10xgenomics_PBMC_5k_peaks_classification_5/analysis_test_sampled.R
Ascripts/10xgenomics_PBMC_5k_peaks_classification_5/classification_peaks_sampled.sh
A(dir)scripts/10xgenomics_PBMC_5k_peaks_classification_6/
Ascripts/10xgenomics_PBMC_5k_peaks_classification_6/analysis_test_sampled.R
Ascripts/10xgenomics_PBMC_5k_peaks_classification_6/classification_peaks_sampled.sh
A(dir)scripts/10xgenomics_PBMC_5k_peaks_classification_7/
Vscripts/{10xgenomics_PBMC_5k_peaks_classification_7/analysis_test.R ← 10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.R}
Ascripts/10xgenomics_PBMC_5k_peaks_classification_7/classification_peaks.sh
Mscripts/bulk_sequencing/analysis_cluster_ctcf_dnase_k562.R
Mscripts/bulk_sequencing/analysis_cluster_ctcf_mnase_k562.R
Mscripts/bulk_sequencing/cluster_ctcf_dnase_k562.sh
Mscripts/bulk_sequencing/cluster_ctcf_mnase_k562.sh
Mscripts/functions.R
A(dir)scripts/genomes/
Ascripts/genomes/hg19.sh
Ascripts/install_libraries/install_libUnitTest++.sh
Ascripts/install_libraries/install_libboost.sh
Mscripts/install_libraries/run_all.sh
Ascripts/install_programs/install_bedtools.sh
Dscripts/install_programs/install_deeptools.sh
Mscripts/install_programs/run_all.sh
A(dir)scripts/pwm/
Ascripts/pwm/reformat_jaspar_2018.sh
Ascripts/pwm/reformat_jaspar_2018_clustering.sh
A(dir)scripts/pwm_tools/
Ascripts/pwm_tools/extract_transfac_pwm.py
Mscripts/run_all.sh
Ascripts/test.R
Ascripts/test/analysis_test_sampled.R
Dscripts/test/test.sh
Ascripts/test/test_1kb.sh
Ascripts/test/test_1kb_pwms.sh
Ascripts/test/test_1kb_sampled.sh
Ascripts/test/test_1kb_sampled_pwms.sh
Ascripts/test/test_2kb.sh
Ascripts/test/test_2kb_sampled.sh
A(dir)scripts/test_2/
Ascripts/test_2/analysis_test_2_sampled.R
Ascripts/test_2/test_1kb_sampled.sh
Ascripts/test_2/test_2kb_sampled.sh
Ascripts/test_dendrogram.R
Psrc/Applications/ChIPPartitioningApplication.cpp
Copied to multiple locations:
src/Applications/EMJointApplication.cpp
src/Applications/EMReadApplication.cpp
Psrc/Applications/ChIPPartitioningApplication.hpp
Copied to multiple locations:
src/Applications/EMJointApplication.hpp
src/Applications/EMReadApplication.hpp
src/Applications/EMSequenceApplication.hpp
Msrc/Applications/CorrelationMatrixCreatorApplication.cpp
Psrc/Applications/EMJointApplication.cpp
Copied from src/Applications/ChIPPartitioningApplication.cpp
Psrc/Applications/EMJointApplication.hpp
Copied from src/Applications/ChIPPartitioningApplication.hpp
Psrc/Applications/EMReadApplication.cpp
Copied from src/Applications/ChIPPartitioningApplication.cpp
Psrc/Applications/EMReadApplication.hpp
Copied from src/Applications/ChIPPartitioningApplication.hpp
Asrc/Applications/EMSequenceApplication.cpp
Psrc/Applications/EMSequenceApplication.hpp
Copied from src/Applications/ChIPPartitioningApplication.hpp
Msrc/Applications/ProbToModelApplication.cpp
Asrc/Applications/ReadModelExtenderApplication.cpp
Asrc/Applications/ReadModelExtenderApplication.hpp
Asrc/Applications/SequenceModelExtenderApplication.cpp
Asrc/Applications/SequenceModelExtenderApplication.hpp
Msrc/CMakeLists.txt
Dsrc/Clustering.old
Dsrc/Clustering.old/ClusteringEngine.cpp
Dsrc/Clustering.old/ClusteringEngine.hpp
Dsrc/Clustering.old/EMEngine.cpp
Dsrc/Clustering.old/EMEngine.hpp
Dsrc/Clustering.old/ReferenceComputer.cpp
Dsrc/Clustering.old/ReferenceComputer.hpp
Dsrc/Clustering.old/typedef.hpp
Msrc/Clustering/DataLayer.cpp
Msrc/Clustering/DataLayer.hpp
Asrc/Clustering/EMBase.cpp
Asrc/Clustering/EMBase.hpp
Dsrc/Clustering/EMEngine.cpp
Dsrc/Clustering/EMEngine.cpp.save
Dsrc/Clustering/EMEngine.hpp
Dsrc/Clustering/EMEngine.hpp.save
Asrc/Clustering/EMJoint.cpp
Asrc/Clustering/EMJoint.hpp
Asrc/Clustering/EMRead.cpp
Asrc/Clustering/EMRead.hpp
Asrc/Clustering/EMSequence.cpp
Asrc/Clustering/EMSequence.hpp
Msrc/Clustering/ModelComputer.cpp
Msrc/Clustering/ModelComputer.hpp
Msrc/Clustering/ReadLayer.cpp
Msrc/Clustering/ReadLayer.hpp
Msrc/Clustering/ReadModelComputer.cpp
Msrc/Clustering/ReadModelComputer.hpp
Msrc/Clustering/SequenceLayer.cpp
Msrc/Clustering/SequenceLayer.hpp
Msrc/Clustering/SequenceModelComputer.cpp
Msrc/Clustering/SequenceModelComputer.hpp
Msrc/GenomicTools/CorrelationMatrixCreator.cpp
Msrc/GenomicTools/CorrelationMatrixCreator.hpp
Msrc/GenomicTools/MatrixCreator.cpp
Msrc/GenomicTools/MatrixCreator.hpp
Msrc/GenomicTools/ReadMatrixCreator.hpp
Msrc/GenomicTools/SequenceMatrixCreator.cpp
Msrc/GenomicTools/SequenceMatrixCreator.hpp
Msrc/Matrix/Matrix.hpp
Msrc/Matrix/Matrix2D.hpp
Msrc/Matrix/Matrix3D.hpp
Msrc/Matrix/Matrix4D.hpp
Msrc/Random/Random.cpp
Msrc/Random/Random.hpp
Msrc/Unittests/unittests_genomictools.cpp
Msrc/Unittests/unittests_matrix.cpp
Msrc/Utility/dna_utility.cpp
Msrc/Utility/dna_utility.hpp
Msrc/main_cormat.cpp
Msrc/main_em.cpp
Msrc/main_em2.cpp

R8820:1bfc0a93ba65

View Options

res/A.png.save

View Options

res/C.png.save

View Options

res/G.png.save

View Options

res/T.png.save

View Options

scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif_chr1.R

View Options

scripts/10xgenomics_PBMC_5k/analysis_ctcf_motif_chr1.sh

View Options

scripts/10xgenomics_PBMC_5k/analysis_peaks.sh

View Options

scripts/10xgenomics_PBMC_5k/process_data.sh

View Options

scripts/10xgenomics_PBMC_5k/run_all.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_1/classification_ctcf_motif.R

View Options

scripts/10xgenomics_PBMC_5k_classification_1/classification_ctcf_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_1/classification_ebf1_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_1/classification_myc_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_1/classification_sp1_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_2/classification_ctcf_motif.R

View Options

scripts/10xgenomics_PBMC_5k_classification_2/classification_ctcf_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_2/classification_ebf1_motif.R

View Options

scripts/10xgenomics_PBMC_5k_classification_2/classification_ebf1_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_2/classification_myc_motif.R

View Options

scripts/10xgenomics_PBMC_5k_classification_2/classification_myc_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_2/classification_sp1_motif.R

View Options

scripts/10xgenomics_PBMC_5k_classification_2/classification_sp1_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_3/classification_ctcf_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_3/classification_sp1_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_4/classification_ctcf_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_classification_4/classification_sp1_motif.R

View Options

scripts/10xgenomics_PBMC_5k_classification_4/classification_sp1_motif.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks/analysis_peaks.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks/analysis_peaks_sampled.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_1/analysis_test_sampled.R

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.R

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks_sampled.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_2/analysis_test_sampled.R

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_2/classification_peaks_sampled.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_3/analysis_test_sampled.R

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_3/classification_peaks_sampled.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_4/analysis_test_sampled.R

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_4/classification_peaks_sampled.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_5/analysis_test_sampled.R

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_5/classification_peaks_sampled.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_6/analysis_test_sampled.R

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_6/classification_peaks_sampled.sh

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_7/analysis_test.R

View Options

scripts/10xgenomics_PBMC_5k_peaks_classification_7/classification_peaks.sh

View Options

scripts/bulk_sequencing/analysis_cluster_ctcf_dnase_k562.R

View Options

scripts/bulk_sequencing/analysis_cluster_ctcf_mnase_k562.R

View Options

scripts/bulk_sequencing/cluster_ctcf_dnase_k562.sh

View Options

scripts/bulk_sequencing/cluster_ctcf_mnase_k562.sh

View Options

scripts/functions.R

View Options

scripts/genomes/hg19.sh

View Options

scripts/install_libraries/install_libUnitTest++.sh

View Options

scripts/install_libraries/install_libboost.sh

View Options

scripts/install_libraries/run_all.sh

View Options

scripts/install_programs/install_bedtools.sh

View Options

scripts/install_programs/install_deeptools.sh

View Options

scripts/install_programs/run_all.sh

View Options

scripts/pwm/reformat_jaspar_2018.sh

View Options

scripts/pwm/reformat_jaspar_2018_clustering.sh

View Options

scripts/pwm_tools/extract_transfac_pwm.py

View Options

scripts/run_all.sh

View Options

scripts/test.R

View Options

scripts/test/analysis_test_sampled.R

View Options

scripts/test/test.sh

View Options

scripts/test/test_1kb.sh

View Options

scripts/test/test_1kb_pwms.sh

View Options

scripts/test/test_1kb_sampled.sh

View Options

scripts/test/test_1kb_sampled_pwms.sh

View Options

scripts/test/test_2kb.sh

View Options

scripts/test/test_2kb_sampled.sh

View Options

scripts/test_2/analysis_test_2_sampled.R

View Options

scripts/test_2/test_1kb_sampled.sh

View Options

scripts/test_2/test_2kb_sampled.sh

View Options

scripts/test_dendrogram.R

View Options

src/Applications/ChIPPartitioningApplication.cpp

View Options

src/Applications/ChIPPartitioningApplication.hpp

View Options

src/Applications/CorrelationMatrixCreatorApplication.cpp

View Options

src/Applications/EMJointApplication.cpp

View Options

src/Applications/EMJointApplication.hpp

View Options

src/Applications/EMReadApplication.cpp

View Options

src/Applications/EMReadApplication.hpp

View Options

src/Applications/EMSequenceApplication.cpp

View Options

src/Applications/EMSequenceApplication.hpp

View Options

src/Applications/ProbToModelApplication.cpp

View Options

src/Applications/ReadModelExtenderApplication.cpp

View Options

src/Applications/ReadModelExtenderApplication.hpp

View Options

src/Applications/SequenceModelExtenderApplication.cpp

View Options

src/Applications/SequenceModelExtenderApplication.hpp

View Options

src/CMakeLists.txt

View Options

src/Clustering.old

View Options

src/Clustering.old/ClusteringEngine.cpp

View Options

src/Clustering.old/ClusteringEngine.hpp

View Options

src/Clustering.old/EMEngine.cpp

View Options

src/Clustering.old/EMEngine.hpp

View Options

src/Clustering.old/ReferenceComputer.cpp

View Options

src/Clustering.old/ReferenceComputer.hpp

View Options

src/Clustering.old/typedef.hpp

View Options

src/Clustering/DataLayer.cpp

View Options

src/Clustering/DataLayer.hpp

View Options

src/Clustering/EMBase.cpp

View Options

src/Clustering/EMBase.hpp

View Options

src/Clustering/EMEngine.cpp

View Options

src/Clustering/EMEngine.cpp.save

View Options

src/Clustering/EMEngine.hpp

View Options

src/Clustering/EMEngine.hpp.save

View Options

src/Clustering/EMJoint.cpp

View Options

src/Clustering/EMJoint.hpp

View Options

src/Clustering/EMRead.cpp

View Options

src/Clustering/EMRead.hpp

View Options

src/Clustering/EMSequence.cpp

View Options

src/Clustering/EMSequence.hpp

View Options

src/Clustering/ModelComputer.cpp

View Options

src/Clustering/ModelComputer.hpp

View Options

src/Clustering/ReadLayer.cpp

View Options

src/Clustering/ReadLayer.hpp

View Options

src/Clustering/ReadModelComputer.cpp

View Options

src/Clustering/ReadModelComputer.hpp

View Options

src/Clustering/SequenceLayer.cpp

View Options

src/Clustering/SequenceLayer.hpp

View Options

src/Clustering/SequenceModelComputer.cpp

View Options

src/Clustering/SequenceModelComputer.hpp

View Options

src/GenomicTools/CorrelationMatrixCreator.cpp

View Options

src/GenomicTools/CorrelationMatrixCreator.hpp

View Options

src/GenomicTools/MatrixCreator.cpp

View Options

src/GenomicTools/MatrixCreator.hpp

View Options

src/GenomicTools/ReadMatrixCreator.hpp

View Options

src/GenomicTools/SequenceMatrixCreator.cpp

View Options

src/GenomicTools/SequenceMatrixCreator.hpp

View Options

src/Matrix/Matrix.hpp

View Options

src/Matrix/Matrix2D.hpp

View Options

src/Matrix/Matrix3D.hpp

View Options

src/Matrix/Matrix4D.hpp

View Options

src/Random/Random.cpp

View Options

src/Random/Random.hpp

View Options

src/Unittests/unittests_genomictools.cpp

View Options

src/Unittests/unittests_matrix.cpp

View Options

src/Utility/dna_utility.cpp

View Options

src/Utility/dna_utility.hpp

View Options

src/main_cormat.cpp

View Options

src/main_em.cpp

View Options

src/main_em2.cpp

c4science · Help