{ "cells": [ { "cell_type": "code", "execution_count": 10, "id": "71b68588", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/icb/yuge.ji/miniconda3/envs/py37/lib/python3.7/site-packages/scanpy/_settings.py:447: DeprecationWarning: `set_matplotlib_formats` is deprecated since IPython 7.23, directly use `matplotlib_inline.backend_inline.set_matplotlib_formats()`\n", " IPython.display.set_matplotlib_formats(*ipython_format)\n" ] } ], "source": [ "import pandas as pd\n", "import matplotlib.pyplot as plt\n", "import scanpy as sc\n", "sc.set_figure_params(dpi=100, frameon=False, color_map='Reds')" ] }, { "cell_type": "markdown", "id": "48d1b033", "metadata": {}, "source": [ "## Statistics on tools\n", "\n", "From scrna-tools.org." ] }, { "cell_type": "code", "execution_count": 3, "id": "32dffb03", "metadata": {}, "outputs": [], "source": [ "df = pd.read_csv('perturbation-tools.tsv', sep='\\t')" ] }, { "cell_type": "code", "execution_count": 4, "id": "1a394f56", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | Tool | \n", "Platform | \n", "Code | \n", "Description | \n", "License | \n", "Added | \n", "Updated | \n", "PlatformR | \n", "PlatformPy | \n", "PlatformCPP | \n", "... | \n", "GHLogins | \n", "GHCommits | \n", "GHIssues | \n", "GHClosedIssues | \n", "GHPctIssuesClosed | \n", "GHMedianResponseDays | \n", "GHMedianClosedDays | \n", "GHIssueActivity | \n", "GHIssueResponse | \n", "GHPopularity | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "Augur | \n", "R | \n", "https://github.com/neurorestore/Augur | \n", "Augur is an R package to prioritize cell types... | \n", "MIT | \n", "2020-01-02 | \n", "2021-07-02 | \n", "True | \n", "False | \n", "False | \n", "... | \n", "NaN | \n", "14.0 | \n", "12.0 | \n", "3.0 | \n", "25.000000 | \n", "1.180486 | \n", "4.585359 | \n", "0.430587 | \n", "3.169630 | \n", "1.431245 | \n", "
| 1 | \n", "Beyondcell | \n", "R | \n", "https://gitlab.com/bu_cnio/beyondcell | \n", "Beyondcell is a computational methodology for ... | \n", "GPL-2.0 | \n", "2021-04-12 | \n", "2021-04-12 | \n", "True | \n", "False | \n", "False | \n", "... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
| 2 | \n", "CellOracle | \n", "python | \n", "https://github.com/morris-lab/CellOracle | \n", "CellOracle integrates single-cell transcriptom... | \n", "Apache-2.0 | \n", "2021-01-25 | \n", "2021-01-25 | \n", "False | \n", "False | \n", "False | \n", "... | \n", "NaN | \n", "257.0 | \n", "59.0 | \n", "57.0 | \n", "96.610169 | \n", "0.385810 | \n", "8.786991 | \n", "1.472808 | \n", "3.655317 | \n", "1.723191 | \n", "
| 3 | \n", "CPA | \n", "Python | \n", "https://github.com/facebookresearch/CPA | \n", "CPA is a deep generative framework to learn ef... | \n", "MIT | \n", "2021-04-16 | \n", "2021-04-16 | \n", "False | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "7.0 | \n", "4.0 | \n", "2.0 | \n", "50.000000 | \n", "0.510862 | \n", "3.944132 | \n", "0.721092 | \n", "3.533387 | \n", "2.549845 | \n", "
| 4 | \n", "MELD | \n", "Python | \n", "https://github.com/KrishnaswamyLab/MELD | \n", "MELD (Manifold Enhancement of Latent Dimension... | \n", "GPL-3.0 | \n", "2019-02-01 | \n", "2021-03-19 | \n", "False | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "336.0 | \n", "11.0 | \n", "9.0 | \n", "81.818182 | \n", "0.703079 | \n", "10.855683 | \n", "0.525024 | \n", "3.394687 | \n", "1.307943 | \n", "
| 5 | \n", "MIMOSCA | \n", "Python | \n", "https://github.com/asncd/MIMOSCA | \n", "Multiple Input Multiple Output Single Cell Ana... | \n", "MIT | \n", "2018-11-15 | \n", "2021-01-12 | \n", "False | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "243.0 | \n", "8.0 | \n", "5.0 | \n", "62.500000 | \n", "0.072697 | \n", "9.958241 | \n", "0.306348 | \n", "4.380176 | \n", "1.441548 | \n", "
| 6 | \n", "MUSIC | \n", "R | \n", "https://github.com/bm2-lab/MUSIC | \n", "MUSIC: Model-based Understanding of SIngle-cel... | \n", "Apache-2.0 | \n", "2019-05-31 | \n", "2021-01-12 | \n", "True | \n", "False | \n", "False | \n", "... | \n", "NaN | \n", "114.0 | \n", "2.0 | \n", "0.0 | \n", "0.000000 | \n", "317.077650 | \n", "NaN | \n", "0.000000 | \n", "0.740525 | \n", "1.175149 | \n", "
| 7 | \n", "PhEMD | \n", "R | \n", "https://github.com/KrishnaswamyLab/phemd | \n", "PhEMD (phenotypic earth mover's distance) iden... | \n", "NaN | \n", "2021-01-25 | \n", "2021-01-25 | \n", "True | \n", "False | \n", "False | \n", "... | \n", "NaN | \n", "10.0 | \n", "5.0 | \n", "5.0 | \n", "100.000000 | \n", "7.549664 | \n", "16.165671 | \n", "0.402925 | \n", "2.363763 | \n", "0.813173 | \n", "
| 8 | \n", "PopAlign | \n", "python | \n", "https://github.com/thomsonlab/popalign | \n", "PopAlign constructs a compressed representatio... | \n", "NaN | \n", "2021-01-25 | \n", "2021-01-25 | \n", "False | \n", "False | \n", "False | \n", "... | \n", "NaN | \n", "265.0 | \n", "5.0 | \n", "3.0 | \n", "60.000000 | \n", "0.679630 | \n", "46.842801 | \n", "0.326758 | \n", "3.409418 | \n", "0.844124 | \n", "
| 9 | \n", "PRESCIENT | \n", "Python | \n", "https://github.com/gifford-lab/prescient | \n", "PRESCIENT (Potential eneRgy undErlying Single ... | \n", "MIT | \n", "2020-09-10 | \n", "2021-06-04 | \n", "False | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "87.0 | \n", "1.0 | \n", "1.0 | \n", "100.000000 | \n", "2.081644 | \n", "6.324039 | \n", "0.283095 | \n", "2.923284 | \n", "1.196050 | \n", "
| 10 | \n", "SCATTome | \n", "R | \n", "https://github.com/bvnlab/SCATTome | \n", "SCATTome (Single Cell Analysis of Targeted Tra... | \n", "GPL-3.0 | \n", "2021-01-25 | \n", "2021-01-25 | \n", "True | \n", "False | \n", "False | \n", "... | \n", "NaN | \n", "26.0 | \n", "1.0 | \n", "1.0 | \n", "100.000000 | \n", "0.256736 | \n", "83.250637 | \n", "0.068492 | \n", "3.832204 | \n", "0.127640 | \n", "
| 11 | \n", "scDEAL | \n", "Python | \n", "https://github.com/OSU-BMBL/scDEAL | \n", "Deep Transfer Learning of Drug Sensitivity by ... | \n", "Apache-2.0 | \n", "2021-08-08 | \n", "2021-08-08 | \n", "False | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "2.0 | \n", "0.0 | \n", "0.0 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "0.000000 | \n", "NaN | \n", "1.700971 | \n", "
| 12 | \n", "scGen | \n", "Python | \n", "https://github.com/theislab/scgen | \n", "scGen is a generative model to predict single-... | \n", "GPL-3.0 | \n", "2019-08-05 | \n", "2021-01-12 | \n", "False | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "361.0 | \n", "42.0 | \n", "42.0 | \n", "100.000000 | \n", "8.797106 | \n", "37.129219 | \n", "1.199783 | \n", "2.297351 | \n", "1.967889 | \n", "
| 13 | \n", "scMAGeCK | \n", "R/Python | \n", "https://bitbucket.org/weililab/scmageck | \n", "scMAGeCK is a computational model to identify ... | \n", "BSD-2-Clause | \n", "2020-02-05 | \n", "2021-01-12 | \n", "True | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
| 14 | \n", "scTenifoldKnk | \n", "R/Python/MATLAB | \n", "https://github.com/cailab-tamu/scTenifoldKnk | \n", "Perform virtual knockout experiments on single... | \n", "GPL-2.0-or-later | \n", "2021-03-26 | \n", "2021-07-27 | \n", "True | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "239.0 | \n", "6.0 | \n", "6.0 | \n", "100.000000 | \n", "0.185932 | \n", "0.594566 | \n", "0.694318 | \n", "3.972337 | \n", "1.061626 | \n", "
| 15 | \n", "trVAE | \n", "Python | \n", "https://github.com/theislab/trVAE | \n", "trVAE is a deep generative model which learns ... | \n", "MIT | \n", "2019-11-03 | \n", "2021-06-28 | \n", "False | \n", "True | \n", "False | \n", "... | \n", "NaN | \n", "843.0 | \n", "10.0 | \n", "8.0 | \n", "80.000000 | \n", "3.857726 | \n", "18.720347 | \n", "0.640489 | \n", "2.655359 | \n", "1.367855 | \n", "
16 rows × 46 columns
\n", "| \n", " | DOI | \n", "Treatment | \n", "Technique | \n", "Shorthand | \n", "Measurement | \n", "# perturbations | \n", "# cell types | \n", "# doses | \n", "# timepoints | \n", "Cell source | \n", "Availability | \n", "Author | \n", "Year | \n", "Raw | \n", "Processed | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "10.1016/j.cell.2016.11.038 | \n", "CRISPR | \n", "Perturb-seq | \n", "Dixit et al (2016) | \n", "RNA-seq | \n", "10,24 | \n", "1 | \n", "- | \n", "1-2 | \n", "TFs followed by LPS treatment in BMDCs, TFs in... | \n", "SCP | \n", "Dixit | \n", "2016 | \n", "https://ndownloader.figshare.com/files/34011689 | \n", "https://ndownloader.figshare.com/files/34014608 | \n", "
| 1 | \n", "10.1126/science.1247651 | \n", "CRISPR | \n", "CRISP-seq | \n", "Jaitin et al (2016) | \n", "RNA-seq | \n", "8-22 | \n", "1 | \n", "- | \n", "1 | \n", "TFs, in vitro hemato and in vivo data. CRISP-s... | \n", "processed | \n", "Jaitin | \n", "2016 | \n", "NaN | \n", "NaN | \n", "
| 2 | \n", "10.1038/nmeth.4177 | \n", "CRISPR | \n", "CROP-seq | \n", "Datlinger et al (2017) | \n", "RNA-seq | \n", "29 | \n", "1 | \n", "- | \n", "1 | \n", "TFs and T-cell receptors pathway targets (3x g... | \n", "processed | \n", "Datlinger | \n", "2017 | \n", "NaN | \n", "NaN | \n", "
| 3 | \n", "10.1038/nmeth.4604 | \n", "CRISPR | \n", "CROP-seq | \n", "Hill et al (2018) | \n", "RNA-seq | \n", "32 | \n", "1 | \n", "2 | \n", "1 | \n", "targeting tumor surpressors in MCF10A with dox... | \n", "processed | \n", "Hill | \n", "2018 | \n", "NaN | \n", "NaN | \n", "
| 4 | \n", "10.1101/2020.11.16.383307 | \n", "CRISPR | \n", "Perturb-seq | \n", "Ursu et al (2020) | \n", "RNA-seq | \n", "200 | \n", "1 | \n", "- | \n", "1 | \n", "100 variants each for 2 genes | \n", "unavailable | \n", "Ursu | \n", "2020 | \n", "NaN | \n", "NaN | \n", "
| 5 | \n", "10.1126/science.aaz6063 | \n", "CRISPR | \n", "Perturb-seq | \n", "Jin et al (2020) | \n", "RNA-seq | \n", "35 | \n", "- | \n", "- | \n", "1 | \n", "in vivo mouse brain development (2x per, frame... | \n", "SCP | \n", "Jin | \n", "2020 | \n", "NaN | \n", "NaN | \n", "
| 6 | \n", "10.1038/s41588-021-00779-1 | \n", "CRISPR | \n", "Perturb-CITE-seq | \n", "Frangieh et al (2021) | \n", "RNA+protein | \n", "248 | \n", "1 | \n", "- | \n", "1 | \n", "treatment resistant cancer samples, patient de... | \n", "SCP | \n", "Frangieh | \n", "2021 | \n", "https://ndownloader.figshare.com/files/34012565 | \n", "https://ndownloader.figshare.com/files/34013717 | \n", "
| 7 | \n", "10.1038/s41592-021-01153-z | \n", "CRISPR KO + antibody | \n", "scifi-RNA-seq | \n", "Datlinger et al (2021) | \n", "RNA-seq | \n", "96 | \n", "1 | \n", "1 | \n", "1 | \n", "20 target genes (2x gRNA per) in Jurkat cells,... | \n", "GSE168620 | \n", "Datlinger | \n", "2021 | \n", "NaN | \n", "NaN | \n", "
| 8 | \n", "10.1126/science.aax4438 | \n", "CRISPRa | \n", "Perturb-seq | \n", "Norman et al (2019) | \n", "RNA-seq | \n", "287 | \n", "1 | \n", "- | \n", "1 | \n", "induction of gene pair targets+single gene con... | \n", "processed | \n", "Norman | \n", "2019 | \n", "https://ndownloader.figshare.com/files/34002548 | \n", "https://ndownloader.figshare.com/files/34027562 | \n", "
| 9 | \n", "10.1016/j.cell.2016.11.048 | \n", "CRISPRi | \n", "Perturb-seq | \n", "Adamson et al (2016) | \n", "RNA-seq | \n", "9-93 (sgRNA) | \n", "1 | \n", "- | \n", "1 | \n", "contains combinatorial guide delivery. Perturb... | \n", "processed | \n", "Adamson | \n", "2016 | \n", "NaN | \n", "NaN | \n", "
| 10 | \n", "10.1016/j.cell.2018.11.029 | \n", "CRISPRi | \n", "CROP-seq | \n", "Gasperini et al (2019) | \n", "RNA-seq | \n", "1119, 5779 | \n", "1 | \n", "- | \n", "1 | \n", "2 experiments, CRISPRi of enhancer region | \n", "processed | \n", "Gasperini | \n", "2019 | \n", "NaN | \n", "NaN | \n", "
| 11 | \n", "10.1038/s41592-020-0837-5 | \n", "CRISPRi | \n", "TAP-seq | \n", "Schraivogel et al (2020) | \n", "RNA-seq | \n", "1778 (enhancers) | \n", "1 | \n", "- | \n", "1 | \n", "targeted enhancers on two chromosomes in K562 ... | \n", "processed | \n", "Schraivogel | \n", "2020 | \n", "NaN | \n", "NaN | \n", "
| 12 | \n", "10.1038/s41587-019-0387-5 | \n", "CRISPRi | \n", "Perturb-seq | \n", "Jost et al (2020) | \n", "RNA-seq | \n", "25 | \n", "2 | \n", "- | \n", "1 | \n", "4 experiments, sgRNA variants with mismatch | \n", "processed | \n", "Jost | \n", "2020 | \n", "NaN | \n", "NaN | \n", "
| 13 | \n", "10.1038/s41588-021-00778-2 | \n", "CRISPR | \n", "ECCITE-seq | \n", "Papalexi et al (2021) | \n", "RNA-seq | \n", "111 (sgRNA) | \n", "1 | \n", "2 | \n", "- | \n", "IFNg, DAC, and TGFb induced THP-1 cells, analy... | \n", "processed | \n", "Papalexi | \n", "2021 | \n", "NaN | \n", "NaN | \n", "
| 14 | \n", "10.1016/j.cels.2020.06.004 | \n", "CRISPRa | \n", "- | \n", "Alda-Catalinas et al (2020) | \n", "RNA-seq | \n", "230 | \n", "1 | \n", "- | \n", "- | \n", "zygotic genomic activation factors in mouse ES... | \n", "GSE135621 | \n", "Alda-Catalinas | \n", "2020 | \n", "NaN | \n", "NaN | \n", "
| 15 | \n", "10.1101/2021.08.23.457400 | \n", "CRISPRi | \n", "CROP-seq | \n", "Leng et al (2021) | \n", "RNA-seq | \n", "30 | \n", "1 | \n", "2 | \n", "- | \n", "IL-1α+TNF+C1q in human IPSC-derived astrocytes | \n", "GSE182308 | \n", "Leng | \n", "2021 | \n", "NaN | \n", "NaN | \n", "
| 16 | \n", "NaN | \n", "genetic targets | \n", "NaN | \n", "Replogle et al (2020) | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "Replogle | \n", "2020 | \n", "NaN | \n", "NaN | \n", "
| 17 | \n", "10.1101/2021.12.16.473013v3 | \n", "genetic targets | \n", "Perturb-seq | \n", "Replogle et al (2021) | \n", "RNA-seq | \n", ">10000 | \n", "2 | \n", "- | \n", "- | \n", "NaN | \n", "upon publication | \n", "Replogle | \n", "2021 | \n", "NaN | \n", "NaN | \n", "
| 18 | \n", "10.1126/science.aax6234 | \n", "small molecules | \n", "sci-Plex | \n", "Srivatsan et al (2019) | \n", "RNA-seq | \n", "188 | \n", "3 | \n", "4 | \n", "2 | \n", "in vitro cancer cell lines and small molecules | \n", "processed | \n", "Srivatsan | \n", "2019 | \n", "https://ndownloader.figshare.com/files/33979517 | \n", "NaN | \n", "
| 19 | \n", "10.1126/sciadv.aav2249 | \n", "small molecules | \n", "multiplexed | \n", "Shin et al (2019) | \n", "RNA-seq | \n", "45 | \n", "2 | \n", "1 | \n", "1 | \n", "transfected barcodes label perturbation condit... | \n", "unavailable | \n", "Shin | \n", "2019 | \n", "NaN | \n", "NaN | \n", "
| 20 | \n", "10.1038/s41467-020-17440-w | \n", "small molecules | \n", "MIX-seq | \n", "McFarland et al (2020) | \n", "RNA-seq | \n", "1-13 | \n", "24-99 | \n", "1 | \n", "1-5 | \n", "4 small molecule experiments, one genetic | \n", "processed | \n", "McFarland | \n", "2020 | \n", "NaN | \n", "NaN | \n", "
| 21 | \n", "10.1038/s41592-019-0689-z | \n", "small molecules | \n", "CyTOF | \n", "Chen et al (2020) | \n", "protein | \n", "300 | \n", "1 | \n", "1 | \n", "1 | \n", "breast cancer cells undergoing TGF-β-induc... | \n", "- | \n", "Chen | \n", "2020 | \n", "NaN | \n", "NaN | \n", "
| 22 | \n", "10.1101/2020.04.22.056341 | \n", "small molecules | \n", "scRNA-seq | \n", "Zhao et al (2020) | \n", "RNA-seq | \n", "2,6 | \n", "6,1 | \n", "- | \n", "- | \n", "compounds applied to patient resections | \n", "processed | \n", "Zhao | \n", "2020 | \n", "NaN | \n", "NaN | \n", "