README

ZhangGroup-MITChemistry · Sep 30, 2023 · 8891e39 · 8891e39
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diff --git a/tutorials/HFF_100KB/.README.md.swp b/tutorials/HFF_100KB/.README.md.swp
diff --git a/tutorials/HFF_100KB/NuclearDeformation/.gitignore b/tutorials/HFF_100KB/NuclearDeformation/.gitignore
@@ -1 +1,2 @@
 simulation.py
+.ipynb_checkpoints
diff --git a/tutorials/HFF_100KB/README.md b/tutorials/HFF_100KB/README.md
@@ -1,6 +1,6 @@
 ## HFF model with nuclear landmarks at 100KB resolution
 
-This folder provides tutorials for setting up and performing simulations of the HFF nucleusi at the 100KB resolution with the presence of various nuclear landmarks, including nuclear lamina, speckles, and nucleoli.
+This folder provides tutorials for setting up and performing simulations of the HFF nucleus at the 100KB resolution with the presence of various nuclear landmarks, including nuclear lamina, speckles, and nucleoli.
 
 - SphericalNucleus
     1. This tutorial explains how to setup simulations of a spherical nucleus.

diff --git a/tutorials/HFF_100KB/SphericalNucleus/.gitignore b/tutorials/HFF_100KB/SphericalNucleus/.gitignore
@@ -1 +1,2 @@
 simulation.py
+.ipynb_checkpoints
diff --git a/tutorials/HFF_100KB/SphericalNucleus/.ipynb_checkpoints/simulation-checkpoint.ipynb b/tutorials/HFF_100KB/SphericalNucleus/.ipynb_checkpoints/simulation-checkpoint.ipynb
diff --git a/tutorials/HFF_100KB/SphericalNucleus/README.md b/tutorials/HFF_100KB/SphericalNucleus/README.md
@@ -0,0 +1,5 @@
+## Spherical Nucleus
+
+This folder provides tutorials for setting up and performing simulations of the HFF nucleus at the 100KB resolution with the presence of various nuclear landmarks, including nuclear lamina, speckles, and nucleoli.
+
+
diff --git a/tutorials/analysis_code/README.md b/tutorials/analysis_code/README.md
@@ -1,13 +1,13 @@
 ## Analysis code
 
-compute_contact_prob.ipynb: call and computes the contact probabilities (DamID, TSASeq, and chr-chr)
+- compute_contact_prob.ipynb: call and computes the contact probabilities (DamID, TSASeq, and chr-chr)
 
-contact_calculation: execution file compiled from Fortran code "../../openNucleome/utility/chromosome_contact_calculation.f90"
+- contact_calculation: execution file compiled from Fortran code "../../openNucleome/utility/chromosome_contact_calculation.f90"
 
-mol_info: store all the molecular information files necessary for computing contact probabilities
+- mol_info: store all the molecular information files necessary for computing contact probabilities
 
-frame_10.dcd: trajectory file example which contains 10 frames
+- frame_10.dcd: trajectory file example which contains 10 frames
 
-contact_prob: store all the chromosome-chromosome contact probabilities, the number of contacts, and the number of analyzed frames
+- contact_prob: store all the chromosome-chromosome contact probabilities, the number of contacts, and the number of analyzed frames
 
-expt_constraints_HFF_100KB.txt: experimental chromosome-chromosome contact probabilities, the first 2489 values are ideal contacts, the next 6 are compt-compt contacts, and the remaining 231 are interchromosomal contacts
+- expt_constraints_HFF_100KB.txt: experimental chromosome-chromosome contact probabilities, the first 2489 values are ideal contacts, the next 6 are compt-compt contacts, and the remaining 231 are interchromosomal contacts
diff --git a/tutorials/analysis_code/contact_prob/README.md b/tutorials/analysis_code/contact_prob/README.md
@@ -1,7 +1,7 @@
 ## contact_prob
 
-contact_prob.txt: averaged contact probabilities over different frames
+- contact_prob.txt: averaged contact probabilities over different frames
 
-nframes.txt: the number of analyzed frames
+- nframes.txt: the number of analyzed frames
 
-counter.txt: the total number of contacts
+- counter.txt: the total number of contacts
diff --git a/tutorials/analysis_code/mol_info/README.md b/tutorials/analysis_code/mol_info/README.md
@@ -1,17 +1,17 @@
 ## Molecular information
 
-DAM-ID_HFF_100KB.txt: DamID signal for HFF model at resolution of 100KB
+- DAM-ID_HFF_100KB.txt: DamID signal for HFF model at resolution of 100KB
 
-TSA-Seq_SON_HFF_100KB.txt: TSA-Seq signal for HFF model at resolution of 100KB
+- TSA-Seq_SON_HFF_100KB.txt: TSA-Seq signal for HFF model at resolution of 100KB
 
-gLengthFile.txt: The difference between each two neighboring values in the file represents the length of the chromosome
+- gLengthFile.txt: The difference between each two neighboring values in the file represents the length of the chromosome
 
-maternalIdxFile.txt: Index of each maternal chromosome
+- maternalIdxFile.txt: Index of each maternal chromosome
 
-paternalIdxFile.txt: Index of each paternal chromosome
+- paternalIdxFile.txt: Index of each paternal chromosome
 
-compartment_genome_100KB_diploid_HFF.txt: The type of each chromatin bead (1: compartment A, 2: compartment B, 3: compartment C, 4: beads around type 3)
+- compartment_genome_100KB_diploid_HFF.txt: The type of each chromatin bead (1: compartment A, 2: compartment B, 3: compartment C, 4: beads around type 3)
 
-mol_index_cell_type-HFF.txt: Index of the chromosome that each bead belongs to
+- mol_index_cell_type-HFF.txt: Index of the chromosome that each bead belongs to
 
-tad_index_genome_100KB_diploid_cell_type-HFF.txt: The first column is the index of each bead in the diploid representation and the second column is the index in the haploid representation
+- tad_index_genome_100KB_diploid_cell_type-HFF.txt: The first column is the index of each bead in the diploid representation and the second column is the index in the haploid representation
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		## Spherical Nucleus

		This folder provides tutorials for setting up and performing simulations of the HFF nucleus at the 100KB resolution with the presence of various nuclear landmarks, including nuclear lamina, speckles, and nucleoli.