README.md
setup.py
data/RNA16.dbn
data/RNA16.react
data/RNA20.dbn
data/RNA20.react
data/RNA21.csv
data/RNA21.dbn
data/__init__.py
data/RNA16_original_data/RNA16_format.py
data/RNA16_original_data/RNA16_dotbracket/23sRNA.bpseq
data/RNA16_original_data/RNA16_dotbracket/5srRNA.bpseq
data/RNA16_original_data/RNA16_dotbracket/ADDRSW.bpseq
data/RNA16_original_data/RNA16_dotbracket/Adenin.bpseq
data/RNA16_original_data/RNA16_dotbracket/GLYCFN.bpseq
data/RNA16_original_data/RNA16_dotbracket/MDLOOP.bpseq
data/RNA16_original_data/RNA16_dotbracket/R009.bpseq
data/RNA16_original_data/RNA16_dotbracket/RNAsp.bpseq
data/RNA16_original_data/RNA16_dotbracket/TRP4.bpseq
data/RNA16_original_data/RNA16_dotbracket/Z-CID.bpseq
data/RNA16_original_data/RNA16_dotbracket/Z-GLY.bpseq
data/RNA16_original_data/RNA16_dotbracket/Z-HCV.bpseq
data/RNA16_original_data/RNA16_dotbracket/p546.bpseq
data/RNA16_original_data/RNA16_dotbracket/srRNA-8.bpseq
data/RNA16_original_data/RNA16_dotbracket/tRNA Asp.bpseq
data/RNA16_original_data/RNA16_dotbracket/tRNA-phe.bpseq
data/RNA16_original_data/RNA16_sequences/23sRNA.seq
data/RNA16_original_data/RNA16_sequences/5srRNA.seq
data/RNA16_original_data/RNA16_sequences/ADDRSW.seq
data/RNA16_original_data/RNA16_sequences/GLYCFN.seq
data/RNA16_original_data/RNA16_sequences/MDLOOP.seq
data/RNA16_original_data/RNA16_sequences/R009.seq
data/RNA16_original_data/RNA16_sequences/RNAsep.seq
data/RNA16_original_data/RNA16_sequences/TRP4.seq
data/RNA16_original_data/RNA16_sequences/Z-CIDGMP.seq
data/RNA16_original_data/RNA16_sequences/Z-GLY.seq
data/RNA16_original_data/RNA16_sequences/ZHCV.seq
data/RNA16_original_data/RNA16_sequences/adenin.seq
data/RNA16_original_data/RNA16_sequences/p546.seq
data/RNA16_original_data/RNA16_sequences/sRNA.seq
data/RNA16_original_data/RNA16_sequences/tRNAPhe.seq
data/RNA16_original_data/RNA16_sequences/trna-asp.seq
data/RNA16_original_data/RNA16_shape/23sRNA.shape
data/RNA16_original_data/RNA16_shape/5srRNA.shape
data/RNA16_original_data/RNA16_shape/ADDRSW.shape
data/RNA16_original_data/RNA16_shape/GLYCFN.shape
data/RNA16_original_data/RNA16_shape/MDLOOP.shape
data/RNA16_original_data/RNA16_shape/R009.shape
data/RNA16_original_data/RNA16_shape/RNAsep.shape
data/RNA16_original_data/RNA16_shape/TRP5.shape
data/RNA16_original_data/RNA16_shape/Z-CIDGMP-1.shape
data/RNA16_original_data/RNA16_shape/ZGLY.shape
data/RNA16_original_data/RNA16_shape/ZHCV.shape
data/RNA16_original_data/RNA16_shape/adenin.shape
data/RNA16_original_data/RNA16_shape/p564.shape
data/RNA16_original_data/RNA16_shape/srRNA.shape
data/RNA16_original_data/RNA16_shape/tRNA-asp.shape
data/RNA16_original_data/RNA16_shape/tRNAphe.shape
data/RNA20_knots_original_data/RNA20_format.py
data/RNA20_knots_original_data/dotbracket/16S-Ecoli.bpseq
data/RNA20_knots_original_data/dotbracket/23S.bpseq
data/RNA20_knots_original_data/dotbracket/5srRNA.bpseq
data/RNA20_knots_original_data/dotbracket/Adenine.bpseq
data/RNA20_knots_original_data/dotbracket/Fuoride.bpseq
data/RNA20_knots_original_data/dotbracket/Group1.bpseq
data/RNA20_knots_original_data/dotbracket/Group1T.bpseq
data/RNA20_knots_original_data/dotbracket/Group2.bpseq
data/RNA20_knots_original_data/dotbracket/HIV.bpseq
data/RNA20_knots_original_data/dotbracket/Hepatits.bpseq
data/RNA20_knots_original_data/dotbracket/Lysine.bpseq
data/RNA20_knots_original_data/dotbracket/M-Box.bpseq
data/RNA20_knots_original_data/dotbracket/P546.bpseq
data/RNA20_knots_original_data/dotbracket/Pre-Q1.bpseq
data/RNA20_knots_original_data/dotbracket/RNAsep.bpseq
data/RNA20_knots_original_data/dotbracket/SAMI.bpseq
data/RNA20_knots_original_data/dotbracket/SingleReg.bpseq
data/RNA20_knots_original_data/dotbracket/Telomerse.bpseq
data/RNA20_knots_original_data/dotbracket/tRNA-asp.bpseq
data/RNA20_knots_original_data/dotbracket/tRNA-phe.bpseq
data/RNA20_knots_original_data/seq/16S-Ecoli.bpseq
data/RNA20_knots_original_data/seq/23S.bpseq
data/RNA20_knots_original_data/seq/5srRNA.bpseq
data/RNA20_knots_original_data/seq/Adenine.bpseq
data/RNA20_knots_original_data/seq/Fuoride.bpseq
data/RNA20_knots_original_data/seq/Group1.bpseq
data/RNA20_knots_original_data/seq/Group1T.bpseq
data/RNA20_knots_original_data/seq/Group2.bpseq
data/RNA20_knots_original_data/seq/HIV.bpseq
data/RNA20_knots_original_data/seq/Hepatits.bpseq
data/RNA20_knots_original_data/seq/Lysine.bpseq
data/RNA20_knots_original_data/seq/M-Box.bpseq
data/RNA20_knots_original_data/seq/P546.bpseq
data/RNA20_knots_original_data/seq/Pre-Q1.bpseq
data/RNA20_knots_original_data/seq/RNAsep.bpseq
data/RNA20_knots_original_data/seq/SAMI.bpseq
data/RNA20_knots_original_data/seq/SingleReg.bpseq
data/RNA20_knots_original_data/seq/Telomerse.bpseq
data/RNA20_knots_original_data/seq/tRNA-asp.bpseq
data/RNA20_knots_original_data/seq/tRNA-phe.bpseq
data/RNA20_knots_original_data/shape/16S-Ecoli.shape
data/RNA20_knots_original_data/shape/23S.shape
data/RNA20_knots_original_data/shape/5srRNA.shape
data/RNA20_knots_original_data/shape/Adenine.shape
data/RNA20_knots_original_data/shape/Fluoride.shape
data/RNA20_knots_original_data/shape/Group1.shape
data/RNA20_knots_original_data/shape/Group1T.shape
data/RNA20_knots_original_data/shape/Group2.shape
data/RNA20_knots_original_data/shape/HIV.shape
data/RNA20_knots_original_data/shape/Hepatits.shape
data/RNA20_knots_original_data/shape/Lysine.shape
data/RNA20_knots_original_data/shape/M-Box.shape
data/RNA20_knots_original_data/shape/P546.shape
data/RNA20_knots_original_data/shape/Pre-Q1.shape
data/RNA20_knots_original_data/shape/RNAsep.shape
data/RNA20_knots_original_data/shape/SAMI.shape
data/RNA20_knots_original_data/shape/SingleReg.shape
data/RNA20_knots_original_data/shape/Telomerase.shape
data/RNA20_knots_original_data/shape/tRNA-asp.shape
data/RNA20_knots_original_data/shape/tRNA-phe.shape
data/eval_rrna/galaxy31.fasta
data/eval_rrna/galaxy31.rawreact
data/eval_rrna/galaxy31.react
data/weeks194_orig/.subopt_cache
data/weeks194_orig/__init__.py
data/weeks194_orig/calcsubopt.py
data/weeks194_orig/cellfree.dbn
data/weeks194_orig/cellfree.react
data/weeks194_orig/cellfree_genes.dbn
data/weeks194_orig/cellfree_genes.react
data/weeks194_orig/collect_subopt.py
data/weeks194_orig/incell.dbn
data/weeks194_orig/incell.react
data/weeks194_orig/incell_genes.dbn
data/weeks194_orig/incell_genes.react
data/weeks194_orig/kasugamycin.dbn
data/weeks194_orig/kasugamycin.react
data/weeks194_orig/kasugamycin_genes.dbn
data/weeks194_orig/kasugamycin_genes.react
data/weeks194_orig/remove_genes.py
data/weeks194_orig/sge_subopt.sh
data/weeks194_orig/translationefficiency.csv
data/weeks194_orig/weeksdatareader.py
notebooks/01_intro.ipynb
notebooks/02_regression_parameter.ipynb
notebooks/03_accessibility.ipynb
notebooks/04_accuracy.ipynb
notebooks/05_proba_real_stru.ipynb
notebooks/06_50seq_accessibility.ipynb
notebooks/07_reactivity_value_boxplots.ipynb
notebooks/08_TranslationEfficiency.ipynb
notebooks/09_struct_vs_nostruct.ipynb
notebooks/FilteringData.ipynb
notebooks/PREDICT_ON_SEQ.ipynb
notebooks/RNAshapes_representatives.ipynb
notebooks/access.py
notebooks/access_PAPER.csv
notebooks/accura.py
notebooks/accuracy_PAPER.csv
notebooks/notebook_helper.py
notebooks/reactivity_value_boxplots.ipynb
notebooks/rrna_evaluation.ipynb
notebooks/shape.ipynb
shaker/ShaKerUp.py
shaker/__init__.py
shaker/_version.py
shaker/simushape.py
shaker/optimization/__init__.py
shaker/optimization/optimize_eden.py
shaker/optimization/optimize_forest.py
shaker/optimization/optimize_forest.sh
shaker/optimization/optimize_gboost.sh
shaker/optimization/optimize_gradient_boosting.py
shaker/optimization/weeks_select.py
shaker/rna_tools/__init__.py
shaker/rna_tools/rna_accuracy.py
shaker/rna_tools/rna_io.py
shaker/rna_tools/rnafold.py
shaker/rna_tools/rnaplfold.py
shaker/rna_tools/rnashapes.py
shaker/rna_tools/rnastructure.py
shaker/rna_tools/rnasubopt.py
shaker/rna_tools/structureprobability.py
shaker/rna_tools/sukosd.py
shaker/rna_tools/util.py
shaker_rna.egg-info/PKG-INFO
shaker_rna.egg-info/SOURCES.txt
shaker_rna.egg-info/dependency_links.txt
shaker_rna.egg-info/entry_points.txt
shaker_rna.egg-info/requires.txt
shaker_rna.egg-info/top_level.txt