In [10]:

import pandas as pd
import matplotlib.pyplot as plt
import scanpy as sc
sc.set_figure_params(dpi=100, frameon=False, color_map='Reds')

/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()`
  IPython.display.set_matplotlib_formats(*ipython_format)

Statistics on tools¶

From scrna-tools.org.

In [3]:

df = pd.read_csv('perturbation-tools.tsv', sep='\t')

In [4]:

df

Out[4]:

	Tool	Platform	Code	Description	License	Added	Updated	PlatformR	PlatformPy	PlatformCPP	...	GHLogins	GHCommits	GHIssues	GHClosedIssues	GHPctIssuesClosed	GHMedianResponseDays	GHMedianClosedDays	GHIssueActivity	GHIssueResponse	GHPopularity
0	Augur	R	https://github.com/neurorestore/Augur	Augur is an R package to prioritize cell types...	MIT	2020-01-02	2021-07-02	True	False	False	...	NaN	14.0	12.0	3.0	25.000000	1.180486	4.585359	0.430587	3.169630	1.431245
1	Beyondcell	R	https://gitlab.com/bu_cnio/beyondcell	Beyondcell is a computational methodology for ...	GPL-2.0	2021-04-12	2021-04-12	True	False	False	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
2	CellOracle	python	https://github.com/morris-lab/CellOracle	CellOracle integrates single-cell transcriptom...	Apache-2.0	2021-01-25	2021-01-25	False	False	False	...	NaN	257.0	59.0	57.0	96.610169	0.385810	8.786991	1.472808	3.655317	1.723191
3	CPA	Python	https://github.com/facebookresearch/CPA	CPA is a deep generative framework to learn ef...	MIT	2021-04-16	2021-04-16	False	True	False	...	NaN	7.0	4.0	2.0	50.000000	0.510862	3.944132	0.721092	3.533387	2.549845
4	MELD	Python	https://github.com/KrishnaswamyLab/MELD	MELD (Manifold Enhancement of Latent Dimension...	GPL-3.0	2019-02-01	2021-03-19	False	True	False	...	NaN	336.0	11.0	9.0	81.818182	0.703079	10.855683	0.525024	3.394687	1.307943
5	MIMOSCA	Python	https://github.com/asncd/MIMOSCA	Multiple Input Multiple Output Single Cell Ana...	MIT	2018-11-15	2021-01-12	False	True	False	...	NaN	243.0	8.0	5.0	62.500000	0.072697	9.958241	0.306348	4.380176	1.441548
6	MUSIC	R	https://github.com/bm2-lab/MUSIC	MUSIC: Model-based Understanding of SIngle-cel...	Apache-2.0	2019-05-31	2021-01-12	True	False	False	...	NaN	114.0	2.0	0.0	0.000000	317.077650	NaN	0.000000	0.740525	1.175149
7	PhEMD	R	https://github.com/KrishnaswamyLab/phemd	PhEMD (phenotypic earth mover's distance) iden...	NaN	2021-01-25	2021-01-25	True	False	False	...	NaN	10.0	5.0	5.0	100.000000	7.549664	16.165671	0.402925	2.363763	0.813173
8	PopAlign	python	https://github.com/thomsonlab/popalign	PopAlign constructs a compressed representatio...	NaN	2021-01-25	2021-01-25	False	False	False	...	NaN	265.0	5.0	3.0	60.000000	0.679630	46.842801	0.326758	3.409418	0.844124
9	PRESCIENT	Python	https://github.com/gifford-lab/prescient	PRESCIENT (Potential eneRgy undErlying Single ...	MIT	2020-09-10	2021-06-04	False	True	False	...	NaN	87.0	1.0	1.0	100.000000	2.081644	6.324039	0.283095	2.923284	1.196050
10	SCATTome	R	https://github.com/bvnlab/SCATTome	SCATTome (Single Cell Analysis of Targeted Tra...	GPL-3.0	2021-01-25	2021-01-25	True	False	False	...	NaN	26.0	1.0	1.0	100.000000	0.256736	83.250637	0.068492	3.832204	0.127640
11	scDEAL	Python	https://github.com/OSU-BMBL/scDEAL	Deep Transfer Learning of Drug Sensitivity by ...	Apache-2.0	2021-08-08	2021-08-08	False	True	False	...	NaN	2.0	0.0	0.0	NaN	NaN	NaN	0.000000	NaN	1.700971
12	scGen	Python	https://github.com/theislab/scgen	scGen is a generative model to predict single-...	GPL-3.0	2019-08-05	2021-01-12	False	True	False	...	NaN	361.0	42.0	42.0	100.000000	8.797106	37.129219	1.199783	2.297351	1.967889
13	scMAGeCK	R/Python	https://bitbucket.org/weililab/scmageck	scMAGeCK is a computational model to identify ...	BSD-2-Clause	2020-02-05	2021-01-12	True	True	False	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
14	scTenifoldKnk	R/Python/MATLAB	https://github.com/cailab-tamu/scTenifoldKnk	Perform virtual knockout experiments on single...	GPL-2.0-or-later	2021-03-26	2021-07-27	True	True	False	...	NaN	239.0	6.0	6.0	100.000000	0.185932	0.594566	0.694318	3.972337	1.061626
15	trVAE	Python	https://github.com/theislab/trVAE	trVAE is a deep generative model which learns ...	MIT	2019-11-03	2021-06-28	False	True	False	...	NaN	843.0	10.0	8.0	80.000000	3.857726	18.720347	0.640489	2.655359	1.367855

16 rows × 46 columns

In [19]:

df.Platform.replace({'python':'Python'}).value_counts().plot(kind='pie', startangle=290)

Out[19]:

<AxesSubplot:ylabel='Platform'>

Statistics on datasets¶

In [27]:

df = pd.read_csv('personal.csv')

In [28]:

df

Out[28]:

	DOI	Treatment	Technique	Shorthand	Measurement	# perturbations	# cell types	# doses	# timepoints	Cell source	Availability	Author	Year	Raw	Processed
0	10.1016/j.cell.2016.11.038	CRISPR	Perturb-seq	Dixit et al (2016)	RNA-seq	10,24	1	-	1-2	TFs followed by LPS treatment in BMDCs, TFs in...	SCP	Dixit	2016	https://ndownloader.figshare.com/files/34011689	https://ndownloader.figshare.com/files/34014608
1	10.1126/science.1247651	CRISPR	CRISP-seq	Jaitin et al (2016)	RNA-seq	8-22	1	-	1	TFs, in vitro hemato and in vivo data. CRISP-s...	processed	Jaitin	2016	NaN	NaN
2	10.1038/nmeth.4177	CRISPR	CROP-seq	Datlinger et al (2017)	RNA-seq	29	1	-	1	TFs and T-cell receptors pathway targets (3x g...	processed	Datlinger	2017	NaN	NaN
3	10.1038/nmeth.4604	CRISPR	CROP-seq	Hill et al (2018)	RNA-seq	32	1	2	1	targeting tumor surpressors in MCF10A with dox...	processed	Hill	2018	NaN	NaN
4	10.1101/2020.11.16.383307	CRISPR	Perturb-seq	Ursu et al (2020)	RNA-seq	200	1	-	1	100 variants each for 2 genes	unavailable	Ursu	2020	NaN	NaN
5	10.1126/science.aaz6063	CRISPR	Perturb-seq	Jin et al (2020)	RNA-seq	35	-	-	1	in vivo mouse brain development (2x per, frame...	SCP	Jin	2020	NaN	NaN
6	10.1038/s41588-021-00779-1	CRISPR	Perturb-CITE-seq	Frangieh et al (2021)	RNA+protein	248	1	-	1	treatment resistant cancer samples, patient de...	SCP	Frangieh	2021	https://ndownloader.figshare.com/files/34012565	https://ndownloader.figshare.com/files/34013717
7	10.1038/s41592-021-01153-z	CRISPR KO + antibody	scifi-RNA-seq	Datlinger et al (2021)	RNA-seq	96	1	1	1	20 target genes (2x gRNA per) in Jurkat cells,...	GSE168620	Datlinger	2021	NaN	NaN
8	10.1126/science.aax4438	CRISPRa	Perturb-seq	Norman et al (2019)	RNA-seq	287	1	-	1	induction of gene pair targets+single gene con...	processed	Norman	2019	https://ndownloader.figshare.com/files/34002548	https://ndownloader.figshare.com/files/34027562
9	10.1016/j.cell.2016.11.048	CRISPRi	Perturb-seq	Adamson et al (2016)	RNA-seq	9-93 (sgRNA)	1	-	1	contains combinatorial guide delivery. Perturb...	processed	Adamson	2016	NaN	NaN
10	10.1016/j.cell.2018.11.029	CRISPRi	CROP-seq	Gasperini et al (2019)	RNA-seq	1119, 5779	1	-	1	2 experiments, CRISPRi of enhancer region	processed	Gasperini	2019	NaN	NaN
11	10.1038/s41592-020-0837-5	CRISPRi	TAP-seq	Schraivogel et al (2020)	RNA-seq	1778 (enhancers)	1	-	1	targeted enhancers on two chromosomes in K562 ...	processed	Schraivogel	2020	NaN	NaN
12	10.1038/s41587-019-0387-5	CRISPRi	Perturb-seq	Jost et al (2020)	RNA-seq	25	2	-	1	4 experiments, sgRNA variants with mismatch	processed	Jost	2020	NaN	NaN
13	10.1038/s41588-021-00778-2	CRISPR	ECCITE-seq	Papalexi et al (2021)	RNA-seq	111 (sgRNA)	1	2	-	IFNg, DAC, and TGFb induced THP-1 cells, analy...	processed	Papalexi	2021	NaN	NaN
14	10.1016/j.cels.2020.06.004	CRISPRa	-	Alda-Catalinas et al (2020)	RNA-seq	230	1	-	-	zygotic genomic activation factors in mouse ES...	GSE135621	Alda-Catalinas	2020	NaN	NaN
15	10.1101/2021.08.23.457400	CRISPRi	CROP-seq	Leng et al (2021)	RNA-seq	30	1	2	-	IL-1α+TNF+C1q in human IPSC-derived astrocytes	GSE182308	Leng	2021	NaN	NaN
16	NaN	genetic targets	NaN	Replogle et al (2020)	NaN	NaN	NaN	NaN	NaN	NaN	NaN	Replogle	2020	NaN	NaN
17	10.1101/2021.12.16.473013v3	genetic targets	Perturb-seq	Replogle et al (2021)	RNA-seq	>10000	2	-	-	NaN	upon publication	Replogle	2021	NaN	NaN
18	10.1126/science.aax6234	small molecules	sci-Plex	Srivatsan et al (2019)	RNA-seq	188	3	4	2	in vitro cancer cell lines and small molecules	processed	Srivatsan	2019	https://ndownloader.figshare.com/files/33979517	NaN
19	10.1126/sciadv.aav2249	small molecules	multiplexed	Shin et al (2019)	RNA-seq	45	2	1	1	transfected barcodes label perturbation condit...	unavailable	Shin	2019	NaN	NaN
20	10.1038/s41467-020-17440-w	small molecules	MIX-seq	McFarland et al (2020)	RNA-seq	1-13	24-99	1	1-5	4 small molecule experiments, one genetic	processed	McFarland	2020	NaN	NaN
21	10.1038/s41592-019-0689-z	small molecules	CyTOF	Chen et al (2020)	protein	300	1	1	1	breast cancer cells undergoing TGF-β-induc...	-	Chen	2020	NaN	NaN
22	10.1101/2020.04.22.056341	small molecules	scRNA-seq	Zhao et al (2020)	RNA-seq	2,6	6,1	-	-	compounds applied to patient resections	processed	Zhao	2020	NaN	NaN

In [29]:

df.Treatment.value_counts().plot(kind='pie', startangle=290)

Out[29]:

<AxesSubplot:ylabel='Treatment'>

In [30]:

df.Technique.value_counts().plot(kind='pie', startangle=290)

Out[30]:

<AxesSubplot:ylabel='Technique'>

In [ ]: