Diffusion scATAC-seq 411e7adaffa4

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Authored by rgroux on Jan 13 2020, 12:51.

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rgroux

Jan 13 2020, 12:51

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rgroux

Jan 13 2020, 13:07

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R8820:f2b641ecc1c6: Added necessary code for EMSequenceApplication and…

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rgroux committed R8820:411e7adaffa4: save (authored by rgroux).Jan 13 2020, 12:51

Changes (74)

		Path
M		scripts/10xgenomics_PBMC_5k/analyse_fragment_lengths.R
M		scripts/10xgenomics_PBMC_5k_motifs/analysis_ctcf_motif.R
M		scripts/10xgenomics_PBMC_5k_motifs/analysis_ctcf_motif.sh
A		scripts/10xgenomics_PBMC_5k_motifs/analysis_ctcf_myc_motif.sh
A		scripts/10xgenomics_PBMC_5k_motifs/analysis_ctcf_sp1_motif.sh
M		scripts/10xgenomics_PBMC_5k_motifs/analysis_ebf1_motif.R
M		scripts/10xgenomics_PBMC_5k_motifs/analysis_myc_motif.R
M		scripts/10xgenomics_PBMC_5k_motifs/analysis_myc_motif.sh
M		scripts/10xgenomics_PBMC_5k_motifs/analysis_sp1_motif.R
M		scripts/10xgenomics_PBMC_5k_motifs/analysis_sp1_motif.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_motifs_classification_0/
P		scripts/10xgenomics_PBMC_5k_motifs_classification_0/classification_ctcf_motif.R Copied from scripts/10xgenomics_PBMC_5k_motifs_classification_1/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_motifs_classification_0/classification_ctcf_motif.sh
P		scripts/10xgenomics_PBMC_5k_motifs_classification_0/classification_ebf1_motif.R Copied from scripts/10xgenomics_PBMC_5k_motifs_classification_1/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_motifs_classification_0/classification_ebf1_motif.sh
P		scripts/10xgenomics_PBMC_5k_motifs_classification_0/classification_myc_motif.R Copied from scripts/10xgenomics_PBMC_5k_motifs_classification_1/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_motifs_classification_0/classification_myc_motif.sh
P		scripts/10xgenomics_PBMC_5k_motifs_classification_0/classification_sp1_motif.R Copied from scripts/10xgenomics_PBMC_5k_motifs_classification_1/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_motifs_classification_0/classification_sp1_motif.sh
P		scripts/10xgenomics_PBMC_5k_motifs_classification_0/run_all.sh Copied from scripts/10xgenomics_PBMC_5k_motifs_classification_1/run_all.sh
M		scripts/10xgenomics_PBMC_5k_motifs_classification_2/classification_ctcf_motif.sh
M		scripts/10xgenomics_PBMC_5k_motifs_classification_2/classification_ebf1_motif.sh
M		scripts/10xgenomics_PBMC_5k_motifs_classification_2/classification_myc_motif.sh
M		scripts/10xgenomics_PBMC_5k_motifs_classification_3/classification_ctcf_motif.sh
M		scripts/10xgenomics_PBMC_5k_motifs_classification_4/classification_ctcf_motif.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_motifs_classification_5/
A		scripts/10xgenomics_PBMC_5k_motifs_classification_5/classification_ctcf_motif.R
A		scripts/10xgenomics_PBMC_5k_motifs_classification_5/classification_ctcf_motif.sh
A		scripts/10xgenomics_PBMC_5k_motifs_classification_5/classification_sp1_motif.R
A		scripts/10xgenomics_PBMC_5k_motifs_classification_5/classification_sp1_motif.sh
P		scripts/10xgenomics_PBMC_5k_motifs_classification_5/run_all.sh Copied from scripts/10xgenomics_PBMC_5k_motifs_classification_4/run_all.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_motifs_classification_6/
A		scripts/10xgenomics_PBMC_5k_motifs_classification_6/analyse_motifs.R
P		scripts/10xgenomics_PBMC_5k_motifs_classification_6/analyse_reads.R Copied from src/GenomicTools/CellMatrixCreator.cpp
A		scripts/10xgenomics_PBMC_5k_motifs_classification_6/classification_motifs.sh
A		scripts/10xgenomics_PBMC_5k_motifs_classification_6/classification_reads.sh
A		scripts/10xgenomics_PBMC_5k_motifs_classification_6/run_all.sh
A	(dir)	scripts/10xgenomics_PBMC_5k_motifs_classification_7/
A		scripts/10xgenomics_PBMC_5k_motifs_classification_7/analyse_motifs.R
A		scripts/10xgenomics_PBMC_5k_motifs_classification_7/classification_motifs.sh
A		scripts/10xgenomics_PBMC_5k_motifs_classification_7/classification_reads.sh
A		scripts/10xgenomics_PBMC_5k_motifs_classification_7/run_all.sh
M		scripts/10xgenomics_PBMC_5k_peaks_classification_0/classification_peaks_sampled.sh
M		scripts/10xgenomics_PBMC_5k_peaks_classification_1/classification_peaks_sampled.sh
M		scripts/10xgenomics_PBMC_5k_peaks_classification_2/classification_peaks_sampled.sh
M		scripts/10xgenomics_PBMC_5k_peaks_classification_3/classification_peaks_sampled.sh
M		scripts/10xgenomics_PBMC_5k_peaks_classification_4/classification_peaks_sampled.sh
M		scripts/10xgenomics_PBMC_5k_peaks_classification_5/classification_peaks_sampled.sh
M		scripts/10xgenomics_PBMC_5k_peaks_classification_7/classification_peaks.R
A	(dir)	scripts/10xgenomics_PBMC_5k_peaks_classification_8/
A		scripts/10xgenomics_PBMC_5k_peaks_classification_8/analysis_test.R
A		scripts/10xgenomics_PBMC_5k_peaks_classification_8/classification_peaks.sh
M		scripts/functions.R
D		scripts/test
D		scripts/test.R
D		scripts/test/analysis_test_sampled.R
D		scripts/test/test_1kb.sh
D		scripts/test/test_1kb_pwms.sh
D		scripts/test/test_1kb_sampled.sh
D		scripts/test/test_1kb_sampled_pwms.sh
D		scripts/test/test_2kb.sh
D		scripts/test/test_2kb_sampled.sh
D		scripts/test_2
D		scripts/test_2/analysis_test_2_sampled.R
D		scripts/test_2/test_1kb_sampled.sh
D		scripts/test_2/test_2kb_sampled.sh
A		scripts/toy_data/analyse_data_sequence.R
A		scripts/toy_data/analysis_data_sequence.sh
M		scripts/toy_data/generate_matrix_data_sequence.R
D		src/Applications/.ProbToModelApplication.cpp.swp
M		src/Applications/EMConsensusSequenceApplication.cpp
M		src/Applications/EMSequenceApplication.cpp
M		src/Clustering/EMBase.cpp
M		src/Clustering/EMConsensusSequence.cpp