├── CONTRIBUTING.md ├── Example_notebook.ipynb ├── LICENSE ├── LICENSE.md ├── README.md ├── data ├── clusters.csv └── exprs_mat.csv ├── docs ├── Makefile ├── _build │ ├── doctrees │ │ ├── api.doctree │ │ ├── basic_usage.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ ├── installation.doctree │ │ ├── references.doctree │ │ └── tutorials.doctree │ └── html │ │ ├── _sources │ │ ├── api.rst.txt │ │ ├── basic_usage.rst.txt │ │ ├── index.rst.txt │ │ ├── installation.rst.txt │ │ ├── references.rst.txt │ │ └── tutorials.rst.txt │ │ ├── _static │ │ ├── Icon.svg │ │ ├── basic.css │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Inconsolata.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ │ ├── img │ │ │ └── Icon.svg │ │ ├── jquery-3.2.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── api.html │ │ ├── basic_usage.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── installation.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── references.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── tutorials.html ├── _static │ └── img │ │ └── Icon.svg ├── api.rst ├── basic_usage.rst ├── conf.py ├── index.rst ├── installation.rst ├── make.bat ├── references.rst └── tutorials.rst ├── requirements.txt ├── resVAE ├── __init__.py ├── config.py ├── reporting.py ├── resvae.py └── utils.py └── setup.py /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # Contributing 2 | 3 | We would like to encourage anyone to contribute to resVAE, but ask you to observe some general rules: 4 | 5 | 1. If you find any bugs, we ask you to use the Issues tab. This allows us to keep track in a more orderly fashion. 6 | 2. Please contact us about your ideas and pull requests prior to submitting them. You can do so through the issue tracker. 7 | 3. Documentation is key! If you make changes to the API, please use docstrings so our Documentation can be updated automatically. 8 | 4. If basic functionality is introduced or changed by your pull request, please update the Readme and any examples accordingly. 9 | 5. When incrementing version numbers, please stick to [SemVer](https://semver.org/) 10 | 11 | Finally, a general note on copyright: This project is GNU GPLv3 licensed, which means that any other projects using resVAE also have to be licensed under the same or a compatible license. We chose this because we believe that Open Source and Open Science are important, and want to facilitate the spread of Open Software. That being said, we do recognize that in some cases there may be licensing clashes. For reasonable requests, we thus reserve the right to grant licenses that differ from the terms laid out in the GNU GPLv3 to individual licensees. By contributing to resVAE, you agree to the following alterations to the license terms: 12 | 13 | * Addition of exceptions, such as GPL linking exceptions 14 | * Granting of exceptions to individual licensees 15 | * Future dual-licensing 16 | 17 | Note that this does not include relicensing - resVAE will remain GPLv3 licensed in any of the above cases. 18 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # resVAE - a restricted latent variational autoencoder 2 | 3 | [![DOI](https://zenodo.org/badge/302657137.svg)](https://zenodo.org/badge/latestdoi/302657137) 4 | 5 | [Paper on Nature Machine Intelligence](https://www.nature.com/articles/s42256-020-00269-9) | [Preprint on BioRxiv](https://www.biorxiv.org/content/10.1101/740415v2) 6 | 7 | resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it. 8 | 9 | * **✨ Update: Check out the new [resVAE ensemble](https://github.com/lab-conrad/resVAE-ensemble)! ✨** 10 | 11 | ## How does resVAE work? 12 | 13 | Briefly, resVAE is not too different from a standard variational autoencoder. In case you are not familiar with artificial neural networks, imagine an algorithm that compresses data, forces the compressed representation to have a specific distribution (in our case, a Gaussian), and decompresses the data again. If you are more familiar with (variational) autoencoders, but fancy a quick reminder, have a look at this excellent [explanation](https://arxiv.org/abs/1906.02691) by Kingma and Welling. 14 | resVAE deviates from this idea in some aspects. One is that we use preclustered data, and feed the identity function of those clusters to the latent space of our network. Thus, we reserve dimensions for individual classes such as cell types, while keeping the encoder and decoder parts of the network the same. In the context of gene expression, this forces the network to learn features that are shared across cell types, but may be more or less active in one cell type or the other. Having reserved dimensions in the latent space allows us to easily map these features to say cell types or disease states. As it turns out, this enables the identification of functional gene sets, including the possibility of correcting this gene set inference for batch effects or treatment groups by encoding these in the latent variable space. 15 | 16 | For more information regarding resVAE, please read our [BioRxiv preprint](https://www.biorxiv.org/content/10.1101/740415v2) or [Nature Machine Intelligence paper](https://www.nature.com/articles/s42256-020-00269-9). 17 | 18 | ## Getting started 19 | 20 | ### Prerequisites and installation 21 | 22 | Although we tried to keep the list of dependencies short, resVAE does require you to download some Python packages. If you are using the install script we provide, these should be handled automatically. This is as easy as downloading the project using `git clone` on the project link (or pressing the button on the top right of the main project page), opening the downloaded folder using a command line, and running: 23 | ``` 24 | pip install -e . 25 | ``` 26 | In case of any issues, you can try forcing pip to install any dependencies first: 27 | ``` 28 | pip install -r requirements.txt 29 | ``` 30 | If this still does not work, try installing the failing packages individually using `conda install ` or `pip install `. 31 | 32 | You can also run resVAE from the project directory without installing it, the options in the example notebook should be fully compatible with this. 33 | 34 | **⚠️ Please note that you would need `tensorflow or tensorflow-gpu version 1` and `keras version < 2.4` to run the current version of resVAE.** 35 | 36 | ### Required input files 37 | 38 | To run resVAE, you will need at the very minimum a single-cell gene expression matrix or something similar where you have a format of *samples x features* or *features x samples*. This should be in some delimited text format, with row and column names included. Ideally, you will also have a file with cluster identities. For a somewhat more complex use case, this could also be several different classes, such as cell type, treatment, disease status, and batch. Each of these variables can then be converted to a one-hot format (resVAE contains utility functions to do this) and concatenated. 39 | 40 | ### Running resVAE 41 | 42 | An example project demonstrating the workflow of resVAE is [included](Example_notebook.ipynb). A more complete documentation of the API (although this is still very much work in progress) can be found in the `docs/_build/html/` subfolder. 43 | 44 | ## Contributing 45 | 46 | We welcome any contributions to the project, but ask you to adhere to some rules laid out in [CONTRIBUTING.md](CONTRIBUTING.md). 47 | 48 | ## Licensing 49 | 50 | This work is released under the terms of the [GNU GPLv3 license](LICENSE.md). Note that this is a copyleft license, so by using resVAE in your own projects, you agree to license them under a compatible license. In case you are interested in including resVAE or parts of its code in your own projects but cannot comply with this, please contact us directly. 51 | 52 | -------------------------------------------------------------------------------- /data/clusters.csv: -------------------------------------------------------------------------------- 1 | ,Barcode,Cluster 2 | 13,AAAGTAGCAGCGTAAG-1,CS 3 | 18,AAATGCCGTACCTACA-1,SC1 4 | 20,AACACGTGTCGCTTCT-1,CS 5 | 22,AACCATGAGATCCGAG-1,CS 6 | 24,AACCGCGCAGGATCGA-1,CS 7 | 28,AACGTTGTCTGCCAGG-1,CS 8 | 29,AACTCAGCAATGGTCT-1,CS 9 | 31,AACTCAGTCGACGGAA-1,CS 10 | 43,AAGCCGCAGTTCGCAT-1,CS 11 | 47,AAGGTTCTCTTCGAGA-1,CS 12 | 54,AATCGGTCAGGGAGAG-1,SC1 13 | 55,AATCGGTGTATAGTAG-1,SC1 14 | 58,ACACCAATCGCTTAGA-1,CS 15 | 60,ACACCCTGTAGGACAC-1,CS 16 | 71,ACAGCCGGTTTGCATG-1,CS 17 | 72,ACAGCTAAGGACATTA-1,SC1 18 | 74,ACATACGAGAAGGCCT-1,CS 19 | 76,ACATACGAGATGGGTC-1,CS 20 | 83,ACCAGTAAGGCTCTTA-1,CS 21 | 86,ACCGTAATCCGCATCT-1,CS 22 | 87,ACCTTTACAGACGCTC-1,SC1 23 | 98,ACGATGTTCCTGCAGG-1,CS 24 | 99,ACGCAGCAGACAGGCT-1,CS 25 | 101,ACGCCAGTCACGCGGT-1,SC1 26 | 102,ACGCCGAAGACCTTTG-1,SC1 27 | 103,ACGCCGAGTACTCAAC-1,CS 28 | 106,ACGGAGACAATGGAGC-1,CS 29 | 107,ACGGAGACATCTACGA-1,CS 30 | 109,ACGGGTCTCTCTTGAT-1,CS 31 | 118,ACTGCTCCACAGACAG-1,SC1 32 | 124,ACTTACTTCCTTGGTC-1,SC1 33 | 126,ACTTGTTAGGGCTTCC-1,CS 34 | 129,AGAATAGAGGGAAACA-1,CS 35 | 131,AGAATAGGTGTCTGAT-1,CS 36 | 135,AGATCTGAGACATAAC-1,CS 37 | 139,AGCAGCCGTTACCGAT-1,CS 38 | 142,AGCCTAAAGAGGTAGA-1,CS 39 | 144,AGCGGTCTCCGTAGGC-1,CS 40 | 145,AGCGGTCTCGTACGGC-1,CS 41 | 148,AGCGTATCAATGAATG-1,CS 42 | 150,AGCGTCGAGCCGGTAA-1,CS 43 | 154,AGCTCTCAGGTGACCA-1,CS 44 | 155,AGCTCTCGTACCATCA-1,CS 45 | 158,AGCTTGAAGACCGGAT-1,CS 46 | 159,AGCTTGACACAAGACG-1,CS 47 | 160,AGGCCACGTAGCAAAT-1,SC1 48 | 173,AGTAGTCCAGGCTCAC-1,CS 49 | 177,AGTCTTTAGTGTTGAA-1,CS 50 | 182,AGTGAGGGTGGAAAGA-1,CS 51 | 188,AGTGGGACATCTCGCT-1,CS 52 | 192,AGTGTCAGTGTGCCTG-1,CS 53 | 196,AGTTGGTGTAAGGGCT-1,CS 54 | 198,AGTTGGTTCCCTCTTT-1,CS 55 | 200,ATAACGCTCACTCCTG-1,SC1 56 | 201,ATAACGCTCCGGGTGT-1,CS 57 | 206,ATAGACCGTTCCACGG-1,CS 58 | 209,ATCACGATCTTCGAGA-1,CS 59 | 212,ATCATCTGTACCCAAT-1,SC1 60 | 213,ATCATCTGTCCCTACT-1,CS 61 | 230,ATCTGCCGTTACGACT-1,CS 62 | 232,ATGAGGGCATCCTTGC-1,CS 63 | 233,ATGCGATAGACAGGCT-1,CS 64 | 237,ATGTGTGTCGTCGTTC-1,CS 65 | 238,ATGTGTGTCTCCAGGG-1,CS 66 | 239,ATTACTCGTGCCTTGG-1,CS 67 | 243,ATTATCCGTTCTGGTA-1,CS 68 | 246,ATTCTACTCGGCGGTT-1,CS 69 | 247,ATTGGACGTTAAGTAG-1,CS 70 | 249,ATTTCTGGTGAGGCTA-1,CS 71 | 262,CAAGAAATCTAACTGG-1,CS 72 | 264,CAAGGCCAGCGAAGGG-1,CS 73 | 265,CAAGGCCAGTACCGGA-1,SC1 74 | 269,CAAGTTGTCTGTTTGT-1,CS 75 | 270,CACAAACAGACGCACA-1,CS 76 | 274,CACACAAAGAGATGAG-1,CS 77 | 275,CACACAAGTGTCTGAT-1,CS 78 | 277,CACACTCAGGATATAC-1,CS 79 | 285,CACAGTAGTTCCGGCA-1,CS 80 | 286,CACAGTATCTTGTATC-1,CS 81 | 287,CACATAGAGTACGCGA-1,SC1 82 | 293,CACCACTAGCTATGCT-1,SC1 83 | 297,CACCACTTCTACTATC-1,CS 84 | 307,CAGAATCGTGCTGTAT-1,CS 85 | 311,CAGATCATCAAGCCTA-1,CS 86 | 312,CAGCAGCAGCGATCCC-1,CS 87 | 318,CAGCCGAAGAGGTTAT-1,CS 88 | 326,CAGCTGGGTCTTGATG-1,CS 89 | 327,CAGTAACAGCAGCCTC-1,CS 90 | 331,CAGTCCTCAGGGTACA-1,CS 91 | 335,CATATTCCAAGACGTG-1,CS 92 | 336,CATATTCGTCTCACCT-1,CS 93 | 340,CATCAAGGTACCATCA-1,CS 94 | 358,CATTATCTCTGGTGTA-1,CS 95 | 366,CCAATCCTCTGTCTAT-1,SC1 96 | 367,CCACCTAAGACTAGGC-1,SC1 97 | 370,CCACCTATCTACCAGA-1,CS 98 | 373,CCAGCGAGTCTCTTTA-1,CS 99 | 375,CCAGCGATCCAGAGGA-1,SC1 100 | 376,CCATGTCAGATCCTGT-1,CS 101 | 380,CCATTCGCACTCAGGC-1,CS 102 | 386,CCCAGTTGTCTAGGTT-1,CS 103 | 387,CCCAGTTTCATGTGGT-1,CS 104 | 389,CCCAGTTTCGCCTGAG-1,CS 105 | 391,CCCATACAGTGACATA-1,CS 106 | 392,CCCTCCTAGTGTTGAA-1,CS 107 | 394,CCCTCCTGTACCATCA-1,CS 108 | 396,CCGGGATCATCCGGGT-1,SC1 109 | 401,CCGTACTCAGACGCTC-1,CS 110 | 405,CCTAAAGGTCTTCTCG-1,CS 111 | 410,CCTCAGTAGCTTCGCG-1,CS 112 | 414,CCTCTGACAGGTTTCA-1,CS 113 | 417,CCTTACGGTACGAAAT-1,CS 114 | 420,CCTTCGATCACATACG-1,SC1 115 | 422,CCTTTCTGTGATAAGT-1,CS 116 | 423,CCTTTCTTCTGCGTAA-1,CS 117 | 425,CGAATGTAGACTAGGC-1,CS 118 | 428,CGAATGTTCGCCCTTA-1,CS 119 | 432,CGACTTCGTTGGTAAA-1,CS 120 | 438,CGAGCACGTCTGCGGT-1,CS 121 | 440,CGAGCACTCATAGCAC-1,CS 122 | 447,CGATGGCCATGACGGA-1,CS 123 | 449,CGATGTATCATAAAGG-1,CS 124 | 452,CGCCAAGCATGACGGA-1,CS 125 | 453,CGCGGTAAGTGCTGCC-1,CS 126 | 457,CGCGTTTTCACAAACC-1,CS 127 | 461,CGCTGGACATCTGGTA-1,SC1 128 | 464,CGCTTCACATTTCACT-1,CS 129 | 467,CGGACACGTCATACTG-1,SC1 130 | 472,CGGACGTGTACATGTC-1,CS 131 | 481,CGGAGTCTCCAAACAC-1,CS 132 | 482,CGGCTAGCAGCCAATT-1,CS 133 | 485,CGGGTCAAGTCGTTTG-1,CS 134 | 496,CGTCACTAGTGACTCT-1,CS 135 | 498,CGTCAGGCATTCCTCG-1,CS 136 | 504,CGTCTACAGCGATTCT-1,CS 137 | 511,CGTGAGCGTTCCCGAG-1,CS 138 | 514,CGTGTAAGTGGTTTCA-1,CS 139 | 517,CGTGTCTCACCTGGTG-1,CS 140 | 520,CGTTAGAGTGACCAAG-1,CS 141 | 531,CTAACTTCAACTGCGC-1,CS 142 | 533,CTAACTTCAGTGGAGT-1,CS 143 | 534,CTAAGACAGGGAGTAA-1,CS 144 | 539,CTAATGGCACGAAGCA-1,CS 145 | 541,CTAATGGGTGGCCCTA-1,CS 146 | 542,CTACACCCATGGTCAT-1,CS 147 | 543,CTACACCGTCCGAATT-1,SC1 148 | 550,CTACCCACAACGATCT-1,SC1 149 | 555,CTACGTCAGCAGCCTC-1,CS 150 | 559,CTAGAGTCAAGCGATG-1,CS 151 | 560,CTAGAGTTCGCAAACT-1,CS 152 | 567,CTCAGAACATCTCGCT-1,CS 153 | 569,CTCATTAGTGTCGCTG-1,CS 154 | 570,CTCCTAGAGTAGGTGC-1,SC1 155 | 571,CTCGAAAGTCAGCTAT-1,CS 156 | 572,CTCGAAAGTTTACTCT-1,CS 157 | 573,CTCGAAATCGGCCGAT-1,CS 158 | 587,CTCTAATGTGTTTGGT-1,CS 159 | 588,CTCTAATTCAGGTTCA-1,SC1 160 | 594,CTCTGGTAGTGGTAAT-1,SC1 161 | 597,CTCTGGTTCACGCATA-1,CS 162 | 599,CTGAAACAGTCCTCCT-1,CS 163 | 611,CTGCGGAGTTACGGAG-1,CS 164 | 618,CTTAACTAGCCCGAAA-1,CS 165 | 632,CTTTGCGGTACTTCTT-1,CS 166 | 640,GAACATCCAAACTGCT-1,CS 167 | 649,GAAGCAGAGTCAAGGC-1,CS 168 | 650,GAAGCAGGTCAAAGAT-1,SC1 169 | 652,GAATAAGCACAGTCGC-1,CS 170 | 656,GACACGCCATGCATGT-1,CS 171 | 658,GACACGCTCTCTTATG-1,SC1 172 | 659,GACAGAGCAATTGCTG-1,CS 173 | 661,GACAGAGTCACCGTAA-1,CS 174 | 662,GACCAATAGACAAGCC-1,CS 175 | 664,GACCAATGTTATCCGA-1,CS 176 | 669,GACGCGTGTGGTCTCG-1,CS 177 | 671,GACGGCTAGCCCAACC-1,CS 178 | 672,GACGGCTAGGATGTAT-1,CS 179 | 673,GACGGCTCAATGCCAT-1,CS 180 | 674,GACGTGCAGAGGGATA-1,CS 181 | 680,GACTACAGTCTGGAGA-1,CS 182 | 683,GACTGCGCACGTTGGC-1,CS 183 | 687,GAGCAGACATCCCACT-1,CS 184 | 688,GAGCAGAGTTCACCTC-1,CS 185 | 690,GAGCAGATCCGAATGT-1,CS 186 | 698,GATCAGTCAATGACCT-1,CS 187 | 704,GATCGCGAGAGATGAG-1,CS 188 | 706,GATCGCGGTCAGAATA-1,CS 189 | 708,GATCGTAAGTGACATA-1,CS 190 | 709,GATCGTACAAACCCAT-1,CS 191 | 712,GATCTAGAGATCCCGC-1,CS 192 | 724,GATTCAGCAGCTCGCA-1,CS 193 | 729,GCAATCAGTGTGAATA-1,CS 194 | 731,GCACATACATGAACCT-1,CS 195 | 734,GCACATATCTTCGAGA-1,CS 196 | 737,GCACTCTCATGCCCGA-1,CS 197 | 739,GCAGCCACAATACGCT-1,CS 198 | 743,GCAGCCATCCAGATCA-1,CS 199 | 754,GCCAAATCATCGGACC-1,SC1 200 | 757,GCCAAATTCTCACATT-1,CS 201 | 759,GCCTCTACAACACCTA-1,CS 202 | 767,GCGCAACGTTCCTCCA-1,CS 203 | 769,GCGCAGTCAAGTTAAG-1,CS 204 | 774,GCGCCAATCCTTTCGG-1,CS 205 | 776,GCGCGATGTTCCACTC-1,CS 206 | 781,GCTCCTATCTACCTGC-1,CS 207 | 783,GCTCTGTAGCGTTCCG-1,CS 208 | 787,GCTCTGTGTCATCCCT-1,CS 209 | 789,GCTCTGTTCACGACTA-1,SC1 210 | 798,GCTGGGTGTAGCGCAA-1,CS 211 | 799,GCTGGGTGTTATTCTC-1,SC1 212 | 802,GCTTGAATCGGAAACG-1,CS 213 | 808,GGAACTTTCATGTCCC-1,CS 214 | 821,GGACATTTCAACGAAA-1,CS 215 | 823,GGACGTCGTCCGACGT-1,CS 216 | 824,GGACGTCTCGGACAAG-1,CS 217 | 826,GGAGCAACAGCCACCA-1,CS 218 | 836,GGCCGATCACCTATCC-1,CS 219 | 837,GGCCGATGTATTCTCT-1,CS 220 | 838,GGCCGATGTCGTGGCT-1,SC1 221 | 842,GGCGTGTCAGCTGTAT-1,CS 222 | 843,GGCTCGAAGCAGCCTC-1,CS 223 | 845,GGCTCGACACAGACTT-1,SC1 224 | 866,GGGTTGCCAGCCTATA-1,CS 225 | 875,GGTGCGTTCGAATCCA-1,CS 226 | 879,GGTGTTAGTGTAAGTA-1,CS 227 | 880,GGTGTTAGTTACGGAG-1,CS 228 | 883,GTAACGTAGTGAATTG-1,CS 229 | 885,GTAACGTGTCTTGCGG-1,CS 230 | 886,GTAACTGAGACCACGA-1,CS 231 | 887,GTAACTGTCGTAGATC-1,CS 232 | 894,GTACTTTGTACCGCTG-1,CS 233 | 899,GTAGGCCAGCGATGAC-1,CS 234 | 902,GTATCTTTCAGTCAGT-1,CS 235 | 905,GTCAAGTCATACGCTA-1,CS 236 | 906,GTCAAGTTCGGTTCGG-1,CS 237 | 910,GTCGGGTCAGGTCTCG-1,CS 238 | 912,GTCGGGTGTAGCGATG-1,CS 239 | 915,GTCTTCGCACTCAGGC-1,CS 240 | 921,GTGAAGGGTTGGTAAA-1,CS 241 | 922,GTGAAGGTCTTCGAGA-1,CS 242 | 923,GTGCAGCCACATCCAA-1,CS 243 | 934,GTGTTAGGTCCATCCT-1,SC1 244 | 936,GTGTTAGTCTCTGTCG-1,CS 245 | 939,GTTAAGCGTGGTTTCA-1,SC1 246 | 944,GTTCGGGAGGGAAACA-1,CS 247 | 945,GTTCGGGCAAGCTGTT-1,CS 248 | 951,GTTTCTATCCGCGGTA-1,CS 249 | 953,GTTTCTATCTGGCGTG-1,CS 250 | 954,TAAACCGAGTATCGAA-1,SC1 251 | 955,TAAACCGCATCCTAGA-1,CS 252 | 956,TAAACCGGTGATAAGT-1,SC1 253 | 967,TACAGTGTCAACACAC-1,CS 254 | 969,TACCTATGTTCGTGAT-1,CS 255 | 971,TACCTTATCCGCAGTG-1,CS 256 | 972,TACGGATCACCGCTAG-1,CS 257 | 976,TACGGTAAGCAATCTC-1,CS 258 | 979,TACTCATAGATCTGCT-1,SC1 259 | 988,TACTTGTTCAGCACAT-1,CS 260 | 990,TAGACCAAGGGTTTCT-1,CS 261 | 994,TAGAGCTCACGTTGGC-1,CS 262 | 997,TAGGCATTCGGCGGTT-1,CS 263 | 1002,TAGTTGGGTCCGTTAA-1,CS 264 | 1008,TATCTCATCCATGAAC-1,CS 265 | 1016,TCAACGATCCAAGCCG-1,CS 266 | 1020,TCACAAGGTCGTGGCT-1,SC1 267 | 1026,TCACGAATCAATCACG-1,CS 268 | 1027,TCACGAATCACAACGT-1,CS 269 | 1036,TCAGGATGTCTTCTCG-1,CS 270 | 1037,TCAGGTAGTGACCAAG-1,CS 271 | 1039,TCATTACTCAACACTG-1,CS 272 | 1041,TCATTTGGTCTTCTCG-1,SC1 273 | 1048,TCGAGGCCAAGCCGCT-1,SC1 274 | 1055,TCGCGTTCACCGCTAG-1,CS 275 | 1058,TCGGGACGTCACTTCC-1,CS 276 | 1064,TCGGTAATCCGCTGTT-1,CS 277 | 1066,TCGTACCCAGCCTATA-1,CS 278 | 1069,TCGTAGACAATCTACG-1,CS 279 | 1074,TCTATTGGTAAGTGGC-1,CS 280 | 1077,TCTATTGTCGCCGTGA-1,CS 281 | 1082,TCTCTAATCTGTCTCG-1,CS 282 | 1083,TCTGAGAAGCTAGTGG-1,CS 283 | 1090,TCTTTCCGTCGCATCG-1,CS 284 | 1093,TGAAAGAAGTGGAGTC-1,CS 285 | 1094,TGAAAGACATGCAATC-1,SC1 286 | 1096,TGAAAGAGTCTTGCGG-1,CS 287 | 1098,TGACAACCATACTCTT-1,CS 288 | 1099,TGACAACCATTACGAC-1,CS 289 | 1101,TGACGGCCATCTCCCA-1,CS 290 | 1103,TGACTAGGTCATATGC-1,CS 291 | 1112,TGAGCATAGAATTCCC-1,CS 292 | 1116,TGAGCATCATCGGGTC-1,CS 293 | 1117,TGAGCATGTTTGGCGC-1,CS 294 | 1122,TGAGGGAGTAAGTTCC-1,CS 295 | 1123,TGATTTCAGAATTGTG-1,CS 296 | 1124,TGATTTCAGCTAGTCT-1,CS 297 | 1130,TGCACCTAGTTCCACA-1,CS 298 | 1133,TGCACCTTCCAATGGT-1,CS 299 | 1135,TGCCAAACAGCTATTG-1,CS 300 | 1139,TGCCCTAAGTCCTCCT-1,SC1 301 | 1140,TGCGCAGAGTGTACCT-1,SC1 302 | 1142,TGCGGGTTCGTAGATC-1,CS 303 | 1143,TGCGTGGAGCGAAGGG-1,SC1 304 | 1152,TGGACGCCACCCAGTG-1,SC1 305 | 1154,TGGCGCAAGGCATGTG-1,CS 306 | 1163,TGGTTCCGTGCTCTTC-1,CS 307 | 1165,TGTCCCAAGAATTCCC-1,CS 308 | 1167,TGTGGTAAGTCTCCTC-1,CS 309 | 1171,TGTTCCGGTCCAGTTA-1,SC1 310 | 1174,TTAACTCGTATATGAG-1,CS 311 | 1184,TTCCCAGAGATATACG-1,CS 312 | 1185,TTCCCAGAGCCAGAAC-1,CS 313 | 1186,TTCCCAGCATAACCTG-1,CS 314 | 1187,TTCCCAGTCAGCGACC-1,SC1 315 | 1191,TTCGAAGAGACTGGGT-1,CS 316 | 1198,TTCGGTCTCACATAGC-1,CS 317 | 1199,TTCGGTCTCCAATGGT-1,CS 318 | 1203,TTCTACATCTTGCATT-1,SC1 319 | 1215,TTGGAACCAGACGCCT-1,CS 320 | 1216,TTGGAACGTAAGTGTA-1,SC1 321 | 1218,TTGGAACTCGAGAACG-1,CS 322 | 1221,TTGTAGGCACCGAATT-1,CS 323 | 1222,TTGTAGGGTCACAAGG-1,SC1 324 | 1224,TTTACTGAGGCAAAGA-1,CS 325 | 1225,TTTACTGCACCAGGTC-1,SC1 326 | 1232,TTTGGTTAGTCCAGGA-1,CS 327 | 1233,TTTGGTTGTATCTGCA-1,CS 328 | 1241,AAACCTGTCGCGTAGC-2,CS 329 | 1243,AAACGGGAGCACAGGT-2,CS 330 | 1248,AAAGCAACAAGCTGAG-2,CS 331 | 1249,AAAGCAACAGCCTTGG-2,CS 332 | 1250,AAAGTAGCACAGAGGT-2,CS 333 | 1256,AACACGTTCCACGACG-2,SC1 334 | 1259,AACCATGGTGCACTTA-2,CS 335 | 1272,AAGACCTCAGGACCCT-2,CS 336 | 1274,AAGACCTGTTGGAGGT-2,CS 337 | 1281,AAGGTTCGTTTGCATG-2,CS 338 | 1282,AAGGTTCTCAGGCCCA-2,CS 339 | 1286,AAGTCTGTCAATAAGG-2,SC1 340 | 1287,AATCCAGAGATGTGGC-2,CS 341 | 1288,AATCCAGAGCCAGAAC-2,CS 342 | 1290,AATCCAGCAAGAAGAG-2,CS 343 | 1291,AATCCAGTCATGCTCC-2,SC1 344 | 1295,ACACCAATCGTCTGAA-2,CS 345 | 1299,ACACCGGAGGGCACTA-2,SC1 346 | 1302,ACACTGAAGGCTAGGT-2,SC1 347 | 1307,ACAGCTAAGGCCCTCA-2,CS 348 | 1319,ACATGGTGTTATCACG-2,SC1 349 | 1320,ACATGGTTCCGAAGAG-2,SC1 350 | 1325,ACCCACTCATATGAGA-2,SC1 351 | 1334,ACGAGGAGTAGGGACT-2,SC1 352 | 1340,ACGATGTAGCCTTGAT-2,CS 353 | 1343,ACGATGTTCCGCTGTT-2,CS 354 | 1344,ACGCAGCAGCCACGTC-2,CS 355 | 1346,ACGCAGCGTGGTACAG-2,CS 356 | 1349,ACGGAGAGTAGGCTGA-2,CS 357 | 1352,ACGGCCATCCAAACAC-2,CS 358 | 1353,ACGGCCATCGGAGCAA-2,CS 359 | 1361,ACTATCTGTATGAAAC-2,SC1 360 | 1369,ACTGCTCAGCCCAATT-2,SC1 361 | 1375,ACTTACTAGCTCCCAG-2,SC1 362 | 1381,ACTTTCAGTGCACTTA-2,SC1 363 | 1383,AGAATAGAGATGTCGG-2,SC1 364 | 1385,AGAATAGTCCATTCTA-2,CS 365 | 1387,AGACGTTAGGCGTACA-2,CS 366 | 1388,AGACGTTAGGTCGGAT-2,CS 367 | 1389,AGACGTTCAGATCCAT-2,CS 368 | 1390,AGAGCGATCTCTAAGG-2,CS 369 | 1394,AGAGTGGGTACCGAGA-2,SC1 370 | 1405,AGCGTATGTATGCTTG-2,CS 371 | 1406,AGCGTATTCAGGATCT-2,CS 372 | 1408,AGCTCCTGTACAGTGG-2,CS 373 | 1410,AGCTCCTTCAACTCTT-2,CS 374 | 1411,AGCTCCTTCATAACCG-2,SC1 375 | 1413,AGCTCTCCAGTGACAG-2,SC1 376 | 1421,AGGGTGAAGGTACTCT-2,CS 377 | 1422,AGGGTGAAGTGTTGAA-2,CS 378 | 1425,AGGGTGATCCTTCAAT-2,CS 379 | 1433,AGTAGTCTCTTATCTG-2,CS 380 | 1446,ATAACGCAGCGAGAAA-2,CS 381 | 1451,ATAACGCGTCGGCTCA-2,CS 382 | 1454,ATAAGAGCATGGTTGT-2,CS 383 | 1458,ATAGACCTCGGATGTT-2,CS 384 | 1459,ATAGACCTCTGCGGCA-2,CS 385 | 1463,ATCACGATCCTCTAGC-2,CS 386 | 1464,ATCATCTCATGCTGGC-2,CS 387 | 1466,ATCATCTGTGACCAAG-2,CS 388 | 1469,ATCATGGCAAGAGTCG-2,CS 389 | 1470,ATCCACCAGACTAGAT-2,SC1 390 | 1473,ATCCGAAGTGCCTTGG-2,CS 391 | 1479,ATCTACTGTAATAGCA-2,CS 392 | 1483,ATGAGGGTCTGGGCCA-2,CS 393 | 1488,ATGGGAGGTGGGTCAA-2,CS 394 | 1491,ATTACTCCATTAGGCT-2,CS 395 | 1494,ATTACTCGTAATCACC-2,CS 396 | 1496,ATTATCCTCACGCGGT-2,SC1 397 | 1497,ATTCTACGTCTAAACC-2,SC1 398 | 1505,ATTTCTGCAGATCGGA-2,CS 399 | 1509,CAACCAAGTTGGGACA-2,CS 400 | 1514,CAACCTCTCTGGCGAC-2,CS 401 | 1516,CAACTAGGTCTCACCT-2,CS 402 | 1518,CAACTAGGTTTACTCT-2,CS 403 | 1520,CAAGAAACAGCGTAAG-2,SC1 404 | 1523,CAAGATCCAAGCCATT-2,CS 405 | 1527,CAAGGCCGTATAGGTA-2,CS 406 | 1530,CAAGTTGGTTGTGGCC-2,CS 407 | 1531,CAAGTTGTCCCTGACT-2,SC1 408 | 1533,CACACAAAGACAATAC-2,SC1 409 | 1542,CACAGGCAGCTATGCT-2,SC1 410 | 1544,CACAGGCGTTATCGGT-2,CS 411 | 1545,CACAGGCTCTCGAGTA-2,CS 412 | 1553,CACATTTGTTACCGAT-2,CS 413 | 1565,CACTCCAGTCCAAGTT-2,CS 414 | 1569,CAGAATCGTAAACCTC-2,CS 415 | 1571,CAGAATCTCCTGCCAT-2,CS 416 | 1572,CAGAGAGAGAACAACT-2,CS 417 | 1576,CAGATCAAGTCCCACG-2,CS 418 | 1583,CAGCATAGTAGCACGA-2,CS 419 | 1588,CAGCCGAAGATCGATA-2,CS 420 | 1592,CAGCCGACATCACGAT-2,CS 421 | 1597,CAGCTGGGTACGCACC-2,CS 422 | 1601,CAGGTGCCATGTCTCC-2,CS 423 | 1603,CAGGTGCTCGCACTCT-2,SC1 424 | 1604,CAGTAACAGGAGCGAG-2,CS 425 | 1609,CATATGGTCCTTTCTC-2,CS 426 | 1616,CATCAGAAGTGTTTGC-2,CS 427 | 1619,CATCAGATCAGGTTCA-2,SC1 428 | 1621,CATCAGATCCGAATGT-2,SC1 429 | 1622,CATCCACGTGTGGTTT-2,SC1 430 | 1625,CATCGAAGTTTGGCGC-2,CS 431 | 1635,CATGACAGTTCCGGCA-2,SC1 432 | 1641,CATGGCGAGCAAATCA-2,SC1 433 | 1647,CCAATCCGTCTTGATG-2,CS 434 | 1648,CCAATCCGTTGCTCCT-2,CS 435 | 1653,CCACGGAAGCCAGTAG-2,SC1 436 | 1656,CCACGGACACCAGATT-2,SC1 437 | 1660,CCACTACAGCCACGTC-2,SC1 438 | 1661,CCACTACCAATACGCT-2,CS 439 | 1663,CCATGTCGTACAGTTC-2,SC1 440 | 1666,CCATTCGAGAGTACCG-2,CS 441 | 1669,CCCAATCCACCAGGCT-2,SC1 442 | 1670,CCCAATCGTACAAGTA-2,SC1 443 | 1675,CCCAGTTCAAGGGTCA-2,CS 444 | 1678,CCCAGTTGTTTGGGCC-2,SC1 445 | 1679,CCCAGTTTCGCGCCAA-2,CS 446 | 1681,CCCATACAGAGTCGGT-2,CS 447 | 1684,CCCATACGTCGTCTTC-2,CS 448 | 1685,CCCTCCTGTCTGCAAT-2,SC1 449 | 1690,CCGTACTAGGTGATAT-2,CS 450 | 1692,CCGTACTGTGCCTGGT-2,SC1 451 | 1693,CCGTACTTCGCCCTTA-2,CS 452 | 1699,CCGTTCAGTCTAGCCG-2,SC1 453 | 1702,CCTACACCAGCTGTAT-2,SC1 454 | 1709,CCTACCACATCTCCCA-2,CS 455 | 1712,CCTACCAGTTTGCATG-2,CS 456 | 1725,CCTCTGAAGAGTACCG-2,CS 457 | 1729,CCTCTGATCCCAAGAT-2,CS 458 | 1733,CCTTACGCATGCCTAA-2,CS 459 | 1734,CCTTCCCAGACTACAA-2,CS 460 | 1743,CGAACATTCGCCATAA-2,SC1 461 | 1745,CGAATGTCAAGTCATC-2,SC1 462 | 1747,CGACCTTAGCTAAACA-2,CS 463 | 1750,CGACCTTTCAGGTTCA-2,CS 464 | 1752,CGACTTCTCGGTGTTA-2,CS 465 | 1759,CGAGCACGTTCGCTAA-2,SC1 466 | 1776,CGATTGACAACCGCCA-2,SC1 467 | 1777,CGATTGAGTCAAACTC-2,CS 468 | 1779,CGCCAAGAGGGCTTCC-2,SC1 469 | 1785,CGCTGGAAGACAGACC-2,SC1 470 | 1795,CGGGTCACACTTAAGC-2,SC1 471 | 1796,CGGGTCACAGAAGCAC-2,CS 472 | 1799,CGTAGCGAGGAATGGA-2,CS 473 | 1801,CGTAGCGGTCCTCTTG-2,CS 474 | 1802,CGTAGGCAGTCGTTTG-2,CS 475 | 1809,CGTCAGGGTGGTACAG-2,CS 476 | 1812,CGTCCATGTAAATACG-2,CS 477 | 1813,CGTCTACCACTCAGGC-2,CS 478 | 1816,CGTCTACTCAACGAAA-2,CS 479 | 1826,CGTTCTGGTGCTTCTC-2,SC1 480 | 1837,CTAATGGCACATCTTT-2,CS 481 | 1838,CTAATGGGTCTTGCGG-2,SC1 482 | 1841,CTACACCCAGCGTAAG-2,CS 483 | 1844,CTACCCAAGGTCATCT-2,SC1 484 | 1845,CTACCCATCCAGAAGG-2,CS 485 | 1846,CTACGTCCAGCGTTCG-2,CS 486 | 1849,CTAGAGTAGATCCCAT-2,SC1 487 | 1850,CTAGAGTCATCATCCC-2,CS 488 | 1851,CTAGAGTGTATAATGG-2,SC1 489 | 1854,CTAGCCTTCTATCCCG-2,CS 490 | 1858,CTCACACCATTGAGCT-2,CS 491 | 1869,CTCGGAGAGCCACCTG-2,CS 492 | 1871,CTCGGAGGTTCACGGC-2,CS 493 | 1874,CTCGTACCATCGACGC-2,CS 494 | 1875,CTCGTCAAGCCCGAAA-2,SC1 495 | 1877,CTCGTCATCATGCATG-2,SC1 496 | 1880,CTCTAATAGTCGTACT-2,SC1 497 | 1882,CTCTAATCAGTAAGCG-2,SC1 498 | 1887,CTCTGGTTCGGCCGAT-2,CS 499 | 1888,CTGAAACCACTCGACG-2,CS 500 | 1890,CTGAAACCAGAAGCAC-2,SC1 501 | 1894,CTGAAACTCTACTATC-2,CS 502 | 1897,CTGATAGAGGGAACGG-2,CS 503 | 1898,CTGATAGCAGGCTCAC-2,CS 504 | 1907,CTGGTCTCATTGGGCC-2,CS 505 | 1913,CTGTGCTCACGACTCG-2,CS 506 | 1914,CTGTGCTTCCCTAACC-2,SC1 507 | 1920,CTTAACTTCCAGGGCT-2,SC1 508 | 1926,CTTCTCTGTACGACCC-2,CS 509 | 1932,CTTTGCGAGAGGTACC-2,CS 510 | 1936,GAACATCGTACATGTC-2,CS 511 | 1938,GAACCTAAGTCGATAA-2,SC1 512 | 1941,GAACCTATCGCGATCG-2,CS 513 | 1942,GAACCTATCTGCTTGC-2,CS 514 | 1944,GAACGGACACTTGGAT-2,CS 515 | 1946,GAACGGATCTTGAGGT-2,CS 516 | 1948,GAATAAGCAATCGGTT-2,CS 517 | 1949,GAATAAGCACGCGAAA-2,CS 518 | 1955,GACACGCAGATGTAAC-2,SC1 519 | 1956,GACACGCAGTTTGCGT-2,CS 520 | 1957,GACACGCGTGAGGGTT-2,SC1 521 | 1962,GACAGAGTCGCTTGTC-2,CS 522 | 1968,GACGCGTTCGAATCCA-2,SC1 523 | 1969,GACGGCTAGTCTTGCA-2,CS 524 | 1970,GACGTGCAGCGATGAC-2,CS 525 | 1973,GACGTGCGTGCTCTTC-2,CS 526 | 1977,GACGTTACAGCTGTGC-2,CS 527 | 1996,GAGGTGAGTTCGCTAA-2,SC1 528 | 1997,GAGGTGAGTTGGTTTG-2,CS 529 | 2001,GATCAGTGTTCGTGAT-2,CS 530 | 2005,GATCGTAAGACAAGCC-2,CS 531 | 2011,GATGAGGAGTTGTCGT-2,CS 532 | 2012,GATGCTACAGGGAGAG-2,CS 533 | 2027,GCACATAGTGAAGGCT-2,SC1 534 | 2030,GCACTCTAGTTAACGA-2,SC1 535 | 2036,GCAGCCACACCCATGG-2,CS 536 | 2038,GCAGCCACAGTGGGAT-2,CS 537 | 2040,GCAGCCATCTTTAGGG-2,CS 538 | 2049,GCATGCGTCACGGTTA-2,CS 539 | 2059,GCGACCATCCGCAGTG-2,CS 540 | 2060,GCGAGAAAGTAAGTAC-2,CS 541 | 2062,GCGAGAACATGAACCT-2,CS 542 | 2063,GCGAGAATCTTGTACT-2,CS 543 | 2067,GCGCGATAGTGCGATG-2,CS 544 | 2071,GCGCGATCAGGACCCT-2,CS 545 | 2077,GCTCCTAGTAGCGCTC-2,CS 546 | 2079,GCTCCTATCGGTCCGA-2,SC1 547 | 2090,GCTGCGAGTCCATGAT-2,CS 548 | 2091,GCTGCGATCCACGACG-2,CS 549 | 2101,GGAAAGCGTAGCGCAA-2,SC1 550 | 2103,GGAAAGCGTCAATGTC-2,SC1 551 | 2106,GGAATAAGTTGTCGCG-2,CS 552 | 2109,GGACAGACAAGAAGAG-2,SC1 553 | 2110,GGACAGACAAGGACAC-2,CS 554 | 2113,GGAGCAACATGTTGAC-2,CS 555 | 2114,GGAGCAAGTGTCAATC-2,CS 556 | 2117,GGATTACAGGTGCACA-2,SC1 557 | 2120,GGCAATTCAGGGTATG-2,SC1 558 | 2141,GGGACCTTCTGATACG-2,CS 559 | 2145,GGGATGAGTCACTTCC-2,SC1 560 | 2154,GGGCATCCATGGAATA-2,SC1 561 | 2159,GGGTCTGTCAGCAACT-2,CS 562 | 2162,GGGTTGCGTGATGTGG-2,SC1 563 | 2164,GGTATTGAGGAACTGC-2,SC1 564 | 2172,GGTGCGTCAGTTCATG-2,CS 565 | 2173,GGTGCGTGTGTAATGA-2,SC1 566 | 2175,GTAACTGCATGTCCTC-2,SC1 567 | 2177,GTACGTACAAACAACA-2,CS 568 | 2179,GTACGTAGTGCAACTT-2,CS 569 | 2180,GTACGTATCATGTCCC-2,CS 570 | 2186,GTAGGCCGTCGCTTCT-2,SC1 571 | 2187,GTAGGCCGTGAAATCA-2,CS 572 | 2193,GTAGTCAGTATAGGTA-2,SC1 573 | 2209,GTCGGGTGTCGTTGTA-2,CS 574 | 2212,GTCTCGTGTCTAAAGA-2,CS 575 | 2213,GTCTTCGAGGGTATCG-2,SC1 576 | 2217,GTGCAGCCAAGGGTCA-2,CS 577 | 2218,GTGCAGCTCGACCAGC-2,CS 578 | 2222,GTGCGGTGTCGCATCG-2,SC1 579 | 2225,GTGCTTCAGCGATCCC-2,SC1 580 | 2226,GTGCTTCCACAGGAGT-2,CS 581 | 2230,GTGGGTCTCTCTTGAT-2,SC1 582 | 2231,GTGTGCGCAAATTGCC-2,SC1 583 | 2233,GTGTTAGAGTGGTAGC-2,CS 584 | 2236,GTTACAGCAGCCAGAA-2,SC1 585 | 2237,GTTACAGGTACTTCTT-2,CS 586 | 2243,GTTCGGGCAGTCACTA-2,SC1 587 | 2246,GTTCGGGTCTCTGTCG-2,CS 588 | 2248,GTTCTCGGTTCGAATC-2,SC1 589 | 2254,TAAGAGACAATGAAAC-2,CS 590 | 2268,TACAGTGAGATCCCGC-2,CS 591 | 2270,TACCTATCACAGGTTT-2,CS 592 | 2272,TACCTTAAGATCTGCT-2,CS 593 | 2276,TACGGGCAGAGGTTAT-2,SC1 594 | 2283,TACTCATCAACTTGAC-2,SC1 595 | 2288,TACTTACCATTTGCTT-2,CS 596 | 2289,TACTTACGTAGCTTGT-2,SC1 597 | 2291,TACTTGTAGCGTCAAG-2,SC1 598 | 2297,TAGACCACACAGAGGT-2,CS 599 | 2301,TAGAGCTCATGCCTAA-2,SC1 600 | 2305,TAGCCGGGTGTTCTTT-2,CS 601 | 2319,TATCAGGCAGTATCTG-2,CS 602 | 2320,TATCAGGCATATGAGA-2,SC1 603 | 2321,TATCTCACAGCGATCC-2,CS 604 | 2324,TATGCCCCACCTCGTT-2,CS 605 | 2327,TATGCCCGTTCGCTAA-2,SC1 606 | 2331,TATTACCCACAAGCCC-2,SC1 607 | 2337,TCAACGATCGGCTTGG-2,CS 608 | 2343,TCACAAGTCACCACCT-2,CS 609 | 2348,TCACGAAGTTGATTCG-2,SC1 610 | 2351,TCAGATGTCCAATGGT-2,CS 611 | 2352,TCAGCAAAGCTAGTCT-2,CS 612 | 2354,TCAGCAAGTATGCTTG-2,CS 613 | 2355,TCAGCTCGTCGACTAT-2,CS 614 | 2363,TCATTTGAGTTAGCGG-2,CS 615 | 2366,TCATTTGTCACCGGGT-2,SC1 616 | 2371,TCCCGATTCAGCTCGG-2,CS 617 | 2373,TCGAGGCAGATGTGTA-2,SC1 618 | 2383,TCGGGACCAGTCAGCC-2,CS 619 | 2393,TCTGAGACATTCCTGC-2,CS 620 | 2398,TCTGGAAAGAATCTCC-2,CS 621 | 2402,TCTTCGGAGTTCGCAT-2,SC1 622 | 2408,TGAAAGAAGTCGTACT-2,CS 623 | 2420,TGAGCATTCTGTACGA-2,CS 624 | 2429,TGATTTCAGGCACATG-2,CS 625 | 2432,TGCCAAAAGAAGGTTT-2,CS 626 | 2436,TGCCCTAAGACAGACC-2,CS 627 | 2441,TGCGCAGGTGCCTGCA-2,CS 628 | 2442,TGCGCAGTCATGTCTT-2,SC1 629 | 2443,TGCGCAGTCGCCATAA-2,CS 630 | 2453,TGCTACCTCCGCGGTA-2,CS 631 | 2454,TGCTACCTCTCCTATA-2,CS 632 | 2461,TGGCGCACATGCAACT-2,CS 633 | 2469,TGGGCGTGTACCTACA-2,SC1 634 | 2471,TGGTTAGTCGGACAAG-2,CS 635 | 2475,TGTCCCAAGTGGTAAT-2,SC1 636 | 2480,TGTGGTATCATGTGGT-2,CS 637 | 2481,TGTGGTATCTACCAGA-2,SC1 638 | 2484,TGTGTTTTCCGTTGTC-2,CS 639 | 2491,TTAGGACTCTCACATT-2,SC1 640 | 2493,TTAGGCACATGTAGTC-2,CS 641 | 2501,TTATGCTTCAGCTTAG-2,CS 642 | 2502,TTATGCTTCTTGTACT-2,CS 643 | 2512,TTCTCAAGTGCGAAAC-2,CS 644 | 2518,TTCTTAGTCACGCATA-2,CS 645 | 2519,TTGAACGCAATGGAAT-2,CS 646 | 2522,TTGAACGGTGTGACGA-2,SC1 647 | 2523,TTGAACGTCACCGTAA-2,CS 648 | 2530,TTGCGTCAGAGATGAG-2,SC1 649 | 2532,TTGGCAATCAAGATCC-2,CS 650 | 2533,TTTACTGTCTATCCCG-2,CS 651 | 2537,TTTATGCTCCGCATCT-2,SC1 652 | 2539,TTTCCTCGTGACCAAG-2,CS 653 | 2541,TTTGCGCAGATGCCTT-2,CS 654 | 2546,TTTGGTTGTCCAAGTT-2,SC1 655 | 2550,TTTGTCAGTCCAGTTA-2,CS 656 | 2551,TTTGTCATCTGTCCGT-2,SC1 657 | 2552,TTTGTCATCTTTCCTC-2,CS 658 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /docs/_build/doctrees/api.doctree: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-conrad/resVAE/add46e73ccc7a076db0a5062e675aeceb515f043/docs/_build/doctrees/tutorials.doctree -------------------------------------------------------------------------------- /docs/_build/html/_sources/api.rst.txt: -------------------------------------------------------------------------------- 1 | |project_name| API 2 | ------------------ 3 | 4 | Main class 5 | __________ 6 | .. automodule:: resVAE.resvae 7 | :members: 8 | 9 | Reporting 10 | _________ 11 | .. automodule:: resVAE.reporting 12 | :members: 13 | 14 | Utility functions 15 | _________________ 16 | .. automodule:: resVAE.utils 17 | :members: 18 | 19 | Configuration file 20 | __________________ 21 | .. automodule:: resVAE.config 22 | :members: -------------------------------------------------------------------------------- /docs/_build/html/_sources/basic_usage.rst.txt: -------------------------------------------------------------------------------- 1 | Basic usage 2 | ----------- 3 | -------------------------------------------------------------------------------- /docs/_build/html/_sources/index.rst.txt: -------------------------------------------------------------------------------- 1 | .. resVAE documentation master file, created by 2 | sphinx-quickstart on Fri Jun 21 19:44:03 2019. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to resVAE's documentation! 7 | ================================ 8 | 9 | resVAE is a versatile tool to perform gene set inference from single-cell RNA-Seq data using a deep neural network based on variational autoencoders. For more info on this check out our preprint. 10 | 11 | .. toctree:: 12 | :maxdepth: 2 13 | :caption: Contents: 14 | 15 | tutorials 16 | basic_usage 17 | installation 18 | api 19 | references 20 | 21 | 22 | Indices and tables 23 | ================== 24 | 25 | * :ref:`genindex` 26 | * :ref:`modindex` 27 | * :ref:`search` 28 | -------------------------------------------------------------------------------- /docs/_build/html/_sources/installation.rst.txt: -------------------------------------------------------------------------------- 1 | Installation 2 | ------------ 3 | 4 | Development version 5 | ___________________ 6 | 7 | To install the development version of |project_name|, simply ``git clone`` |project_name| to your local computer, ``cd`` to the root 8 | directory, and run:: 9 | 10 | pip install -e . 11 | 12 | Troubleshooting 13 | _______________ 14 | 15 | If the installation fails, check the `requirements.txt` file for any dependencies you might be missing, or run:: 16 | 17 | pip install -r requirements.txt 18 | 19 | from |project_name|'s root directory. -------------------------------------------------------------------------------- /docs/_build/html/_sources/references.rst.txt: -------------------------------------------------------------------------------- 1 | References 2 | ---------- 3 | 4 | `resVAE on BioRxiv `_. -------------------------------------------------------------------------------- /docs/_build/html/_sources/tutorials.rst.txt: -------------------------------------------------------------------------------- 1 | Tutorials 2 | --------- 3 | -------------------------------------------------------------------------------- /docs/_build/html/_static/Icon.svg: -------------------------------------------------------------------------------- 1 | Icon -------------------------------------------------------------------------------- /docs/_build/html/_static/basic.css: -------------------------------------------------------------------------------- 1 | /* 2 | * basic.css 3 | * ~~~~~~~~~ 4 | * 5 | * Sphinx stylesheet -- basic theme. 6 | * 7 | * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. 8 | * :license: BSD, see LICENSE for details. 9 | * 10 | */ 11 | 12 | /* -- main layout ----------------------------------------------------------- */ 13 | 14 | div.clearer { 15 | clear: both; 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16 | 17 | /** 18 | * make the code below compatible with browsers without 19 | * an installed firebug like debugger 20 | if (!window.console || !console.firebug) { 21 | var names = ["log", "debug", "info", "warn", "error", "assert", "dir", 22 | "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace", 23 | "profile", "profileEnd"]; 24 | window.console = {}; 25 | for (var i = 0; i < names.length; ++i) 26 | window.console[names[i]] = function() {}; 27 | } 28 | */ 29 | 30 | /** 31 | * small helper function to urldecode strings 32 | */ 33 | jQuery.urldecode = function(x) { 34 | return decodeURIComponent(x).replace(/\+/g, ' '); 35 | }; 36 | 37 | /** 38 | * small helper function to urlencode strings 39 | */ 40 | jQuery.urlencode = encodeURIComponent; 41 | 42 | /** 43 | * This function returns the parsed url parameters of the 44 | * current request. Multiple values per key are supported, 45 | * it will always return arrays of strings for the value parts. 46 | */ 47 | jQuery.getQueryParameters = function(s) { 48 | if (typeof s === 'undefined') 49 | s = document.location.search; 50 | var parts = s.substr(s.indexOf('?') + 1).split('&'); 51 | var result = {}; 52 | for (var i = 0; i < parts.length; i++) { 53 | var tmp = parts[i].split('=', 2); 54 | var key = jQuery.urldecode(tmp[0]); 55 | var value = jQuery.urldecode(tmp[1]); 56 | if (key in result) 57 | result[key].push(value); 58 | else 59 | result[key] = [value]; 60 | } 61 | return result; 62 | }; 63 | 64 | /** 65 | * highlight a given string on a jquery object by wrapping it in 66 | * span elements with the given class name. 67 | */ 68 | jQuery.fn.highlightText = function(text, className) { 69 | function highlight(node, addItems) { 70 | if (node.nodeType === 3) { 71 | var val = node.nodeValue; 72 | var pos = val.toLowerCase().indexOf(text); 73 | if (pos >= 0 && 74 | !jQuery(node.parentNode).hasClass(className) && 75 | !jQuery(node.parentNode).hasClass("nohighlight")) { 76 | var span; 77 | var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); 78 | if (isInSVG) { 79 | span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); 80 | } else { 81 | span = document.createElement("span"); 82 | span.className = className; 83 | } 84 | span.appendChild(document.createTextNode(val.substr(pos, text.length))); 85 | node.parentNode.insertBefore(span, node.parentNode.insertBefore( 86 | document.createTextNode(val.substr(pos + text.length)), 87 | node.nextSibling)); 88 | node.nodeValue = val.substr(0, pos); 89 | if (isInSVG) { 90 | var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); 91 | var bbox = node.parentElement.getBBox(); 92 | rect.x.baseVal.value = bbox.x; 93 | rect.y.baseVal.value = bbox.y; 94 | rect.width.baseVal.value = bbox.width; 95 | rect.height.baseVal.value = bbox.height; 96 | rect.setAttribute('class', className); 97 | addItems.push({ 98 | "parent": node.parentNode, 99 | "target": rect}); 100 | } 101 | } 102 | } 103 | else if (!jQuery(node).is("button, select, textarea")) { 104 | jQuery.each(node.childNodes, function() { 105 | highlight(this, addItems); 106 | }); 107 | } 108 | } 109 | var addItems = []; 110 | var result = this.each(function() { 111 | highlight(this, addItems); 112 | }); 113 | for (var i = 0; i < addItems.length; ++i) { 114 | jQuery(addItems[i].parent).before(addItems[i].target); 115 | } 116 | return result; 117 | }; 118 | 119 | /* 120 | * backward compatibility for jQuery.browser 121 | * This will be supported until firefox bug is fixed. 122 | */ 123 | if (!jQuery.browser) { 124 | jQuery.uaMatch = function(ua) { 125 | ua = ua.toLowerCase(); 126 | 127 | var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || 128 | /(webkit)[ \/]([\w.]+)/.exec(ua) || 129 | /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || 130 | /(msie) ([\w.]+)/.exec(ua) || 131 | ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || 132 | []; 133 | 134 | return { 135 | browser: match[ 1 ] || "", 136 | version: match[ 2 ] || "0" 137 | }; 138 | }; 139 | jQuery.browser = {}; 140 | jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; 141 | } 142 | 143 | /** 144 | * Small JavaScript module for the documentation. 145 | */ 146 | var Documentation = { 147 | 148 | init : function() { 149 | this.fixFirefoxAnchorBug(); 150 | this.highlightSearchWords(); 151 | this.initIndexTable(); 152 | if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) { 153 | this.initOnKeyListeners(); 154 | } 155 | }, 156 | 157 | /** 158 | * i18n support 159 | */ 160 | TRANSLATIONS : {}, 161 | PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; }, 162 | LOCALE : 'unknown', 163 | 164 | // gettext and ngettext don't access this so that the functions 165 | // can safely bound to a different name (_ = Documentation.gettext) 166 | gettext : function(string) { 167 | var translated = Documentation.TRANSLATIONS[string]; 168 | if (typeof translated === 'undefined') 169 | return string; 170 | return (typeof translated === 'string') ? translated : translated[0]; 171 | }, 172 | 173 | ngettext : function(singular, plural, n) { 174 | var translated = Documentation.TRANSLATIONS[singular]; 175 | if (typeof translated === 'undefined') 176 | return (n == 1) ? singular : plural; 177 | return translated[Documentation.PLURALEXPR(n)]; 178 | }, 179 | 180 | addTranslations : function(catalog) { 181 | for (var key in catalog.messages) 182 | this.TRANSLATIONS[key] = catalog.messages[key]; 183 | this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')'); 184 | this.LOCALE = catalog.locale; 185 | }, 186 | 187 | /** 188 | * add context elements like header anchor links 189 | */ 190 | addContextElements : function() { 191 | $('div[id] > :header:first').each(function() { 192 | $('\u00B6'). 193 | attr('href', '#' + this.id). 194 | attr('title', _('Permalink to this headline')). 195 | appendTo(this); 196 | }); 197 | $('dt[id]').each(function() { 198 | $('\u00B6'). 199 | attr('href', '#' + this.id). 200 | attr('title', _('Permalink to this definition')). 201 | appendTo(this); 202 | }); 203 | }, 204 | 205 | /** 206 | * workaround a firefox stupidity 207 | * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075 208 | */ 209 | fixFirefoxAnchorBug : function() { 210 | if (document.location.hash && $.browser.mozilla) 211 | window.setTimeout(function() { 212 | document.location.href += ''; 213 | }, 10); 214 | }, 215 | 216 | /** 217 | * highlight the search words provided in the url in the text 218 | */ 219 | highlightSearchWords : function() { 220 | var params = $.getQueryParameters(); 221 | var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : []; 222 | if (terms.length) { 223 | var body = $('div.body'); 224 | if (!body.length) { 225 | body = $('body'); 226 | } 227 | window.setTimeout(function() { 228 | $.each(terms, function() { 229 | body.highlightText(this.toLowerCase(), 'highlighted'); 230 | }); 231 | }, 10); 232 | $('

' + _('Hide Search Matches') + '

') 234 | .appendTo($('#searchbox')); 235 | } 236 | }, 237 | 238 | /** 239 | * init the domain index toggle buttons 240 | */ 241 | initIndexTable : function() { 242 | var togglers = $('img.toggler').click(function() { 243 | var src = $(this).attr('src'); 244 | var idnum = $(this).attr('id').substr(7); 245 | $('tr.cg-' + idnum).toggle(); 246 | if (src.substr(-9) === 'minus.png') 247 | $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); 248 | else 249 | $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); 250 | }).css('display', ''); 251 | if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { 252 | togglers.click(); 253 | } 254 | }, 255 | 256 | /** 257 | * helper function to hide the search marks again 258 | */ 259 | hideSearchWords : function() { 260 | $('#searchbox .highlight-link').fadeOut(300); 261 | $('span.highlighted').removeClass('highlighted'); 262 | }, 263 | 264 | /** 265 | * make the url absolute 266 | */ 267 | makeURL : function(relativeURL) { 268 | return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; 269 | }, 270 | 271 | /** 272 | * get the current relative url 273 | */ 274 | getCurrentURL : function() { 275 | var path = document.location.pathname; 276 | var parts = path.split(/\//); 277 | $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { 278 | if (this === '..') 279 | parts.pop(); 280 | }); 281 | var url = parts.join('/'); 282 | return path.substring(url.lastIndexOf('/') + 1, path.length - 1); 283 | }, 284 | 285 | initOnKeyListeners: function() { 286 | $(document).keyup(function(event) { 287 | var activeElementType = document.activeElement.tagName; 288 | // don't navigate when in search box or textarea 289 | if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') { 290 | switch (event.keyCode) { 291 | case 37: // left 292 | var prevHref = $('link[rel="prev"]').prop('href'); 293 | if (prevHref) { 294 | window.location.href = prevHref; 295 | return false; 296 | } 297 | case 39: // right 298 | var nextHref = $('link[rel="next"]').prop('href'); 299 | if (nextHref) { 300 | window.location.href = nextHref; 301 | return false; 302 | } 303 | } 304 | } 305 | }); 306 | } 307 | }; 308 | 309 | // quick alias for translations 310 | _ = Documentation.gettext; 311 | 312 | $(document).ready(function() { 313 | Documentation.init(); 314 | }); 315 | -------------------------------------------------------------------------------- /docs/_build/html/_static/documentation_options.js: -------------------------------------------------------------------------------- 1 | var DOCUMENTATION_OPTIONS = { 2 | URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), 3 | VERSION: '', 4 | LANGUAGE: 'None', 5 | COLLAPSE_INDEX: false, 6 | FILE_SUFFIX: '.html', 7 | HAS_SOURCE: true, 8 | SOURCELINK_SUFFIX: '.txt', 9 | NAVIGATION_WITH_KEYS: false 10 | }; -------------------------------------------------------------------------------- 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108 | if (re2.test(stem)) { 109 | w = stem; 110 | re2 = /(at|bl|iz)$/; 111 | re3 = new RegExp("([^aeiouylsz])\\1$"); 112 | re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); 113 | if (re2.test(w)) 114 | w = w + "e"; 115 | else if (re3.test(w)) { 116 | re = /.$/; 117 | w = w.replace(re,""); 118 | } 119 | else if (re4.test(w)) 120 | w = w + "e"; 121 | } 122 | } 123 | 124 | // Step 1c 125 | re = /^(.+?)y$/; 126 | if (re.test(w)) { 127 | var fp = re.exec(w); 128 | stem = fp[1]; 129 | re = new RegExp(s_v); 130 | if (re.test(stem)) 131 | w = stem + "i"; 132 | } 133 | 134 | // Step 2 135 | re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; 136 | if (re.test(w)) { 137 | var fp = re.exec(w); 138 | stem = fp[1]; 139 | suffix = fp[2]; 140 | re = new RegExp(mgr0); 141 | if (re.test(stem)) 142 | w = stem + step2list[suffix]; 143 | } 144 | 145 | // Step 3 146 | re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; 147 | if (re.test(w)) { 148 | var fp = re.exec(w); 149 | stem = fp[1]; 150 | suffix = fp[2]; 151 | re = new RegExp(mgr0); 152 | if (re.test(stem)) 153 | w = stem + step3list[suffix]; 154 | } 155 | 156 | // Step 4 157 | re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; 158 | re2 = /^(.+?)(s|t)(ion)$/; 159 | if (re.test(w)) { 160 | var fp = re.exec(w); 161 | stem = fp[1]; 162 | re = new RegExp(mgr1); 163 | if (re.test(stem)) 164 | w = stem; 165 | } 166 | else if (re2.test(w)) { 167 | var fp = re2.exec(w); 168 | stem = fp[1] + fp[2]; 169 | re2 = new RegExp(mgr1); 170 | if (re2.test(stem)) 171 | w = stem; 172 | } 173 | 174 | // Step 5 175 | re = /^(.+?)e$/; 176 | if (re.test(w)) { 177 | var fp = re.exec(w); 178 | stem = fp[1]; 179 | re = new RegExp(mgr1); 180 | re2 = new RegExp(meq1); 181 | re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); 182 | if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) 183 | w = stem; 184 | } 185 | re = /ll$/; 186 | re2 = new RegExp(mgr1); 187 | if (re.test(w) && re2.test(w)) { 188 | re = /.$/; 189 | w = w.replace(re,""); 190 | } 191 | 192 | // and turn initial Y back to y 193 | if (firstch == "y") 194 | w = firstch.toLowerCase() + w.substr(1); 195 | return w; 196 | } 197 | } 198 | 199 | 200 | 201 | 202 | 203 | var splitChars = (function() { 204 | var result = {}; 205 | var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648, 206 | 1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702, 207 | 2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971, 208 | 2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345, 209 | 3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761, 210 | 3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823, 211 | 4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125, 212 | 8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695, 213 | 11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587, 214 | 43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141]; 215 | var i, j, start, end; 216 | for (i = 0; i < singles.length; i++) { 217 | result[singles[i]] = true; 218 | } 219 | var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709], 220 | [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161], 221 | [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568], 222 | [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807], 223 | [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047], 224 | [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383], 225 | [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450], 226 | [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547], 227 | [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673], 228 | [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820], 229 | [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946], 230 | [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023], 231 | [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173], 232 | [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332], 233 | [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481], 234 | [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718], 235 | [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791], 236 | [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095], 237 | [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205], 238 | [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687], 239 | [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968], 240 | [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869], 241 | [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102], 242 | [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271], 243 | [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592], 244 | [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822], 245 | [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167], 246 | [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959], 247 | [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143], 248 | [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318], 249 | [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483], 250 | [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101], 251 | [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567], 252 | [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292], 253 | [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444], 254 | [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783], 255 | [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311], 256 | [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511], 257 | [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774], 258 | [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071], 259 | [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263], 260 | [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519], 261 | [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647], 262 | [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967], 263 | [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295], 264 | [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274], 265 | [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007], 266 | [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381], 267 | [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]]; 268 | for (i = 0; i < ranges.length; i++) { 269 | start = ranges[i][0]; 270 | end = ranges[i][1]; 271 | for (j = start; j <= end; j++) { 272 | result[j] = true; 273 | } 274 | } 275 | return result; 276 | })(); 277 | 278 | function splitQuery(query) { 279 | var result = []; 280 | var start = -1; 281 | for (var i = 0; i < query.length; i++) { 282 | if (splitChars[query.charCodeAt(i)]) { 283 | if (start !== -1) { 284 | result.push(query.slice(start, i)); 285 | start = -1; 286 | } 287 | } else if (start === -1) { 288 | start = i; 289 | } 290 | } 291 | if (start !== -1) { 292 | result.push(query.slice(start)); 293 | } 294 | return result; 295 | } 296 | 297 | 298 | -------------------------------------------------------------------------------- /docs/_build/html/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-conrad/resVAE/add46e73ccc7a076db0a5062e675aeceb515f043/docs/_build/html/_static/minus.png -------------------------------------------------------------------------------- /docs/_build/html/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-conrad/resVAE/add46e73ccc7a076db0a5062e675aeceb515f043/docs/_build/html/_static/plus.png -------------------------------------------------------------------------------- /docs/_build/html/_static/pygments.css: -------------------------------------------------------------------------------- 1 | .highlight .hll { background-color: #ffffcc } 2 | .highlight { background: #f8f8f8; } 3 | .highlight .c { color: #408080; font-style: italic } /* Comment */ 4 | .highlight .err { border: 1px solid #FF0000 } /* Error */ 5 | .highlight .k { color: #008000; font-weight: bold } /* Keyword */ 6 | .highlight .o { color: #666666 } /* Operator */ 7 | .highlight .ch { color: #408080; font-style: italic } /* Comment.Hashbang */ 8 | .highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */ 9 | .highlight .cp { color: #BC7A00 } /* Comment.Preproc */ 10 | .highlight .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */ 11 | .highlight .c1 { color: #408080; font-style: italic } /* Comment.Single */ 12 | .highlight .cs { color: #408080; font-style: italic } /* Comment.Special */ 13 | .highlight .gd { color: #A00000 } /* Generic.Deleted */ 14 | .highlight .ge { font-style: italic } /* Generic.Emph */ 15 | .highlight .gr { color: #FF0000 } /* Generic.Error */ 16 | .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */ 17 | .highlight .gi { color: #00A000 } /* Generic.Inserted */ 18 | .highlight .go { color: #888888 } /* Generic.Output */ 19 | .highlight .gp { color: #000080; 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23 | }, 24 | */ 25 | 26 | // query matches the full name of an object 27 | objNameMatch: 11, 28 | // or matches in the last dotted part of the object name 29 | objPartialMatch: 6, 30 | // Additive scores depending on the priority of the object 31 | objPrio: {0: 15, // used to be importantResults 32 | 1: 5, // used to be objectResults 33 | 2: -5}, // used to be unimportantResults 34 | // Used when the priority is not in the mapping. 35 | objPrioDefault: 0, 36 | 37 | // query found in title 38 | title: 15, 39 | partialTitle: 7, 40 | // query found in terms 41 | term: 5, 42 | partialTerm: 2 43 | }; 44 | } 45 | 46 | if (!splitQuery) { 47 | function splitQuery(query) { 48 | return query.split(/\s+/); 49 | } 50 | } 51 | 52 | /** 53 | * Search Module 54 | */ 55 | var Search = { 56 | 57 | _index : null, 58 | _queued_query : null, 59 | _pulse_status : -1, 60 | 61 | htmlToText : function(htmlString) { 62 | var htmlElement = document.createElement('span'); 63 | htmlElement.innerHTML = htmlString; 64 | $(htmlElement).find('.headerlink').remove(); 65 | docContent = $(htmlElement).find('[role=main]')[0]; 66 | return docContent.textContent || docContent.innerText; 67 | }, 68 | 69 | init : function() { 70 | var params = $.getQueryParameters(); 71 | if (params.q) { 72 | var query = params.q[0]; 73 | $('input[name="q"]')[0].value = query; 74 | this.performSearch(query); 75 | } 76 | }, 77 | 78 | loadIndex : function(url) { 79 | $.ajax({type: "GET", url: url, data: null, 80 | dataType: "script", cache: true, 81 | complete: function(jqxhr, textstatus) { 82 | if (textstatus != "success") { 83 | document.getElementById("searchindexloader").src = url; 84 | } 85 | }}); 86 | }, 87 | 88 | setIndex : function(index) { 89 | var q; 90 | this._index = index; 91 | if ((q = this._queued_query) !== null) { 92 | this._queued_query = null; 93 | Search.query(q); 94 | } 95 | }, 96 | 97 | hasIndex : function() { 98 | return this._index !== null; 99 | }, 100 | 101 | deferQuery : function(query) { 102 | this._queued_query = query; 103 | }, 104 | 105 | stopPulse : function() { 106 | this._pulse_status = 0; 107 | }, 108 | 109 | startPulse : function() { 110 | if (this._pulse_status >= 0) 111 | return; 112 | function pulse() { 113 | var i; 114 | Search._pulse_status = (Search._pulse_status + 1) % 4; 115 | var dotString = ''; 116 | for (i = 0; i < Search._pulse_status; i++) 117 | dotString += '.'; 118 | Search.dots.text(dotString); 119 | if (Search._pulse_status > -1) 120 | window.setTimeout(pulse, 500); 121 | } 122 | pulse(); 123 | }, 124 | 125 | /** 126 | * perform a search for something (or wait until index is loaded) 127 | */ 128 | performSearch : function(query) { 129 | // create the required interface elements 130 | this.out = $('#search-results'); 131 | this.title = $('

' + _('Searching') + '

').appendTo(this.out); 132 | this.dots = $('').appendTo(this.title); 133 | this.status = $('

 

').appendTo(this.out); 134 | this.output = $('