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base repository: BackofenLab/Cherri
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base: v0.1
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head repository: BackofenLab/Cherri
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compare: master
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Showing with 11,142 additions and 1,074 deletions.
  1. +52 −0 .github/workflows/build-sphinx.yml
  2. +7 −0 .gitignore
  3. +24 −0 Makefile
  4. +12 −411 README.md
  5. +12 −0 benchmark/.gitignore
  6. +30 −0 benchmark/README.md
  7. BIN benchmark/RIblast-1.2.0.zip
  8. BIN benchmark/RIsearch-1.2.tar.gz
  9. +20 −0 benchmark/benchmark-calls.txt
  10. BIN benchmark/benchmark-data.xlsx
  11. +161 −0 benchmark/benchmark-stats.R
  12. +76 −0 benchmark/cherri_input.csv
  13. +15 −0 benchmark/extract-fasta.R
  14. BIN benchmark/intaRNA-3.3.2.tar.gz
  15. +76 −0 benchmark/overlap.csv
  16. BIN benchmark/overlap.png
  17. +277 −158 bin/cherri
  18. +35 −20 bin/find_occupied_regions.py
  19. +11 −26 bin/find_trusted_RRI.py
  20. +137 −105 bin/generate_pos_neg_with_context.py
  21. +1 −1 bin/get_features.py
  22. BIN docs/_downloads/a47f3fc5f02580ea9cdf7f17216f17c9/CheRRI-workflow.png
  23. BIN docs/_images/CheRRI-workflow.png
  24. +123 −0 docs/_sources/docs/documentation.md.txt
  25. +279 −0 docs/_sources/docs/usage.md.txt
  26. +147 −0 docs/_sources/docs/welcome.md.txt
  27. +16 −0 docs/_sources/index.md.txt
  28. BIN docs/_static/CheRRI-workflow.png
  29. +123 −0 docs/_static/_sphinx_javascript_frameworks_compat.js
  30. +925 −0 docs/_static/basic.css
  31. +1 −0 docs/_static/css/badge_only.css
  32. BIN docs/_static/css/fonts/Roboto-Slab-Bold.woff
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  36. BIN docs/_static/css/fonts/fontawesome-webfont.eot
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  38. BIN docs/_static/css/fonts/fontawesome-webfont.ttf
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  49. +4 −0 docs/_static/css/theme.css
  50. 0 docs/_static/custom.css
  51. +156 −0 docs/_static/doctools.js
  52. +13 −0 docs/_static/documentation_options.js
  53. BIN docs/_static/file.png
  54. +2 −0 docs/_static/jquery.js
  55. +1 −0 docs/_static/js/badge_only.js
  56. +4 −0 docs/_static/js/html5shiv-printshiv.min.js
  57. +4 −0 docs/_static/js/html5shiv.min.js
  58. +1 −0 docs/_static/js/theme.js
  59. +199 −0 docs/_static/language_data.js
  60. BIN docs/_static/minus.png
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  62. +75 −0 docs/_static/pygments.css
  63. +574 −0 docs/_static/searchtools.js
  64. +154 −0 docs/_static/sphinx_highlight.js
  65. +434 −0 docs/docs/documentation.html
  66. +532 −0 docs/docs/usage.html
  67. +243 −0 docs/docs/welcome.html
  68. +117 −0 docs/genindex.html
  69. +202 −0 docs/index.html
  70. +7 −0 docs/objects.inv
  71. +132 −0 docs/search.html
  72. +1 −0 docs/searchindex.js
  73. BIN plots/CheRRI-workflow.png
  74. BIN plots/features/feature_importance_barplot_full.png
  75. BIN plots/features/feature_importance_barplot_mouse_human.png
  76. +595 −161 rrieval/lib.py
  77. +123 −0 scripts/5_fold_CV_cherri_pipeline.py
  78. +60 −0 scripts/correlation_matrix.py
  79. +1 −1 scripts/create_trainings_data.py
  80. +40 −0 scripts/docs/builddocs.sh
  81. +1 −1 scripts/evaluate_instance.py
  82. +194 −0 scripts/feature_impotrance.py
  83. +160 −0 scripts/graph_feature_occurence.py
  84. +402 −0 scripts/plots/F1_bar_plots.ipynb
  85. BIN scripts/plots/F1_cross_model_plot.pdf
  86. BIN scripts/plots/F1_cross_model_plot_old.pdf
  87. +10 −0 scripts/plots/colour_list
  88. +1 −1 scripts/plots/compute_f1.py
  89. +107 −39 scripts/plots/f1_model_matrix.py
  90. +135 −0 scripts/plots/plot_PRC.py
  91. +1 −1 scripts/plots/plot_tRRIs.py
  92. +6 −7 setup.py
  93. 0 source/assets/CSS/custom.css
  94. BIN source/assets/images/CheRRI-workflow.png
  95. +61 −0 source/conf.py
  96. +123 −0 source/docs/documentation.md
  97. +279 −0 source/docs/usage.md
  98. +147 −0 source/docs/welcome.md
  99. +16 −0 source/index.md
  100. +66 −0 sphinx.yaml
  101. +72 −142 test_data/README.md
  102. 0 test_data/evaluate/{test_evaluate_rris.cvs → test_evaluate_rris.csv}
  103. +4 −0 test_data/training/Paris/data_infos.txt
  104. +452 −0 test_data/training/user_defined.csv
52 changes: 52 additions & 0 deletions .github/workflows/build-sphinx.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
name: build-sphinx-github-pages

env:
GITHUB_ACTOR: BackofenLab
GITHUB_REPOSITORY: BackofenLab/Cherri
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

on:
push:
branches:
- master
paths:
- 'source/**'

# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:

# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
contents: write
pages: write
id-token: write

jobs:
build_sphinx_job:
runs-on: ubuntu-latest
steps:
- name: Get prerequisites and clone repository
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
set -x
sudo apt-get update
sudo apt-get install -y git
git clone "https://token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" .
shell: bash

- name: Run build script for Sphinx-based GitHub Pages
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: "scripts/docs/builddocs.sh"
shell: bash

- name: Upload artifact
uses: actions/upload-pages-artifact@v2
with:
# Upload entire repository
path: 'docs/'

- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v2
7 changes: 7 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
# sphinx build folder
_build
# test files
test_cherri.sh
test_cherri_st_off.sh
.Rproj.user
Cherri.Rproj
24 changes: 24 additions & 0 deletions Makefile
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
# Minimal makefile for Sphinx documentation
#

# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = source
BUILDDIR = _build

# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

.PHONY: help Makefile

github:
@make html
@cp -a _build/html/. ./docs

# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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