Using EPFL template Writting PWMScan part
9f1248a4f530
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Authored by rgroux on Oct 10 2019, 17:54.

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Using EPFL template Writting PWMScan part

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rgroux

Oct 10 2019, 17:54

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rgroux

Oct 17 2019, 15:13

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R9524:2cb4179d12c2: save

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rgroux committed R9524:9f1248a4f530: Using EPFL template Writting PWMScan part (authored by rgroux).Oct 10 2019, 17:54

Changes (116)

		Path
A		README.md
A	(dir)	head/
A		head/abstracts.aux
A		head/abstracts.tex
A		head/acknowledgements.aux
A		head/acknowledgements.tex
A		head/dedication.aux
A		head/dedication.tex
A		head/preface.aux
A		head/preface.tex
A		head/settings_custom.log
A		head/settings_custom.tex
A		head/settings_epfl_template.tex
A		head/titlepage.tex
A	(dir)	images/
A	(dir)	images/ch_atac-seq/
V		{images/ch_atac-seq ← scATAC-seq/figures}/ATAC-seq.png
V		{images/ch_atac-seq ← scATAC-seq/figures}/ATAC-seq2.png
V		{images/ch_atac-seq ← scATAC-seq/figures}/ctcf_motifs_10e-6_aggregations.png
A		images/ch_atac-seq/ctcf_motifs_6class_noshift_flip.png
A		images/ch_atac-seq/ctcf_motifs_6class_shift_flip.png
V		{images/ch_atac-seq ← scATAC-seq/figures}/ctcf_sp1_myc_ebf1_footprint.png
A		images/ch_atac-seq/em.png
V		{images/ch_atac-seq ← scATAC-seq/figures}/em.svg
A		images/ch_atac-seq/fragment_lengths.png
V		{images/ch_atac-seq ← scATAC-seq/figures}/pipeline.png
V		{images/ch_atac-seq ← scATAC-seq/figures}/pipeline.svg
A		images/ch_atac-seq/simulated_sequences_2class_flip_auc_roc.png
A		images/ch_atac-seq/simulated_sequences_2class_flip_best_motifs.png
A		images/ch_atac-seq/sp1_motifs_10class.png
A		images/ch_atac-seq/sp1_motifs_6class_noshift_flip.png
A		images/ch_atac-seq/sp1_motifs_6class_shift_flip.png
A		images/ch_atac-seq/sp1_motifs_7class.png
A	(dir)	images/ch_softwares/
A		images/ch_softwares/figure_s1.png
A		images/ch_softwares/figure_s4.png
A		images/ch_softwares/flowchart.png
A		images/ch_softwares/pwmscan_fig1.png
A		images/epfl.eps
A		images/epfl.pdf
A	(dir)	main/
A		main/ch2_figures_tables.tex
A		main/ch3_math.tex
A		main/ch4_More_text.tex
A		main/ch4_more_text.aux
A		main/ch_atac-seq.aux
A		main/ch_atac-seq.log
V		{main/ch_atac-seq.tex ← phd_thesis.tex}
A		main/ch_encode_peaks.aux
A		main/ch_encode_peaks.tex
A		main/ch_introduction.aux
A		main/ch_introduction.tex
A		main/ch_smile-seq.aux
A		main/ch_smile-seq.tex
A		main/ch_softwares.aux
A		main/ch_softwares.log
A		main/ch_softwares.tex
A		my_thesis.aux
A		my_thesis.bbl
A		my_thesis.blg
A		my_thesis.log
A		my_thesis.pdf
A		my_thesis.synctex.gz
A		my_thesis.tex
A		my_thesis.toc
D		phd_thesis.aux
D		phd_thesis.bbl
V		{phd_thesis.bib → tail/bibliography.bib}
D		phd_thesis.blg
D		phd_thesis.log
D		phd_thesis.pdf
D		phd_thesis.synctex.gz
V		{phd_thesis.tex → main/ch_atac-seq.tex}
D		scATAC-seq
D		scATAC-seq.docx
D		scATAC-seq/figures
V		{scATAC-seq/figures → images/ch_atac-seq}/ATAC-seq.png
V		{scATAC-seq/figures → images/ch_atac-seq}/ATAC-seq2.png
V		{scATAC-seq/figures → images/ch_atac-seq}/ctcf_motifs_10e-6_aggregations.png
V		{scATAC-seq/figures → images/ch_atac-seq}/ctcf_sp1_myc_ebf1_footprint.png
D		scATAC-seq/figures/em.png
V		{scATAC-seq/figures → images/ch_atac-seq}/em.svg
D		scATAC-seq/figures/fragment_lengths_class_prob.png
D		scATAC-seq/figures/fragment_lengths_classes.png
D		scATAC-seq/figures/fragment_lengths_groups.png
V		{scATAC-seq/figures → images/ch_atac-seq}/pipeline.png
V		{scATAC-seq/figures → images/ch_atac-seq}/pipeline.svg
D		scATAC-seq/scATAC-seq_draft.docx
D		scATAC-seq/scripts
V		{scATAC-seq/scripts → scripts/ch_atac-seq}/figure_ctcf_sp1_myc_ebf1_footprint.R
D		scATAC-seq/scripts/get_figures.sh
A	(dir)	scripts/
A	(dir)	scripts/ch_atac-seq/
A		scripts/ch_atac-seq/figure_ctcf_6classes.R
V		{scripts/ch_atac-seq ← scATAC-seq/scripts}/figure_ctcf_sp1_myc_ebf1_footprint.R
A		scripts/ch_atac-seq/figure_sp1_6classes.R
A		scripts/ch_atac-seq/figure_sp1_motifs.R
A		scripts/ch_atac-seq/get_figures.sh
A	(dir)	scripts/ch_softwares/
A		scripts/ch_softwares/get_figures.sh
A	(dir)	tail/
A		tail/appendix.aux
A		tail/appendix.log
A		tail/appendix.tex
A		tail/biblio.aux
A		tail/biblio.tex
V		{tail/bibliography.bib ← phd_thesis.bib}
A		tail/cv.aux
A		tail/cv.pdf
A		tail/cv.tex
A	(dir)	utopia_font/
A		utopia_font/README
A		utopia_font/UtopiaLaTeX-Bold.ttf
A		utopia_font/UtopiaLaTeX-BoldItalic.ttf
A		utopia_font/UtopiaLaTeX-Italic.ttf
A		utopia_font/UtopiaLaTeX-Regular.ttf