Reagent/Resource	Source	Identifier
Dataset
DepMap 2020 Q2 Genome‐wide CRISPR screens	https://figshare.com/articles/DepMap_20Q2_Public/12280541/4	N/A
Achilles_gene_effect.csv	Meyers et al (2017), Dempster et al (2019b), Data ref: Broad DepMap (2020)
sample_info.csv
DepMap 2022 Q4 Genome‐wide CRISPR screens	https://figshare.com/articles/dataset/DepMap_22Q4_Public/21637199/2	N/A
CRISPRGeneEffect.csv	Meyers et al (2017), Dempster et al (2019b, 2021), Pacini et al (2021), Data ref: Broad DepMap (2022)
10x Genomics scRNA‐seq gene expression dataset	https://support.10xgenomics.com/single‐cell‐gene‐expression/datasets/3.0.2/5k_pbmc_v3	N/A
5k_pbmc_v3_filtered_feature_bc_matrix.tar	Data ref: 10x Genomics (2019)
Software
argparse R package v2.0.3	https://cran.r‐project.org/web/packages/argparse/index.html	N/A
	Davis et al (2023)
clusterProfiler R package v3.16.1	Wu et al (2021)	N/A
crfsuite R package v0.4.1	https://cran.r‐project.org/web/packages/crfsuite/index.html	N/A
	Wijffels et al (2022)
cvms R package	https://cran.r‐project.org/web/packages/cvms/index.html	N/A
	Olsen et al (2023)
Cytoscape v3.4.0	Shannon et al (2003)	N/A
devtools R package v2.4.3	https://cran.r‐project.org/web/packages/devtools/index.html	N/A
	Wickham et al (2022)
dplyr R package v1.0.8	https://cran.r‐project.org/web/packages/dplyr/index.html	N/A
	Wickham et al (2023b)
FLEX R package	https://github.com/csbio/FLEX_R	N/A
	Rahman et al (2021)
Generalized least squares (GLS) normalization	https://github.com/kundajelab/coessentiality	N/A
	Wainberg et al (2021)
ggplot2 R package v3.3.5	https://cran.r‐project.org/web/packages/ggplot2/index.html	N/A
	Wickham et al (2023a)
ggthemes R package v4.2.4	https://cran.r‐project.org/web/packages/ggthemes/index.html	N/A
	Arnold et al (2021)
gplots R package v3.1.1	https://cran.r‐project.org/web/packages/gplots/index.html	N/A
	Warnes et al (2022)
gridExtra R package v2.3	https://cran.r‐project.org/web/packages/gridExtra/index.html	N/A
	Auguie & Antonov (2017)
NumPy v1.17.4	https://numpy.org/	N/A
Pandas v0.25.1	https://zenodo.org/record/8239932	N/A
pheatmap R package v1.0.12	https://cran.r‐project.org/web/packages/pheatmap/index.html	N/A
	Kolde (2019)
Python version 3.7.3	https://www.python.org/	N/A
PyTorch v1.6.0	https://pytorch.org/	N/A
R versions 3.6.3 and 4.1.3	https://www.r‐project.org/	N/A
ramify R package v0.3.3	https://cran.r‐project.org/web/packages/ramify/index.html	N/A
	Greenwell (2016)
RColorBrewer R package v1.1–3	https://cran.r‐project.org/web/packages/RColorBrewer/index.html	N/A
	Neuwirth (2022)
RcppCNPy R package v0.2.11	https://cran.r‐project.org/web/packages/RcppCNPy/index.html	N/A
	Eddelbuettel & Wu (2022)
reshape R package v0.8.9	https://cran.r‐project.org/web/packages/reshape/index.html	N/A
	Wickham (2022a)
rpca R package v0.2.3	https://cran.r‐project.org/web/packages/rpca/index.html	N/A
	Candès et al (2011), Sykulski (2015)
Seurat R package v4.3.0	https://cloud.r‐project.org/web/packages/Seurat/index.html	N/A
	Hao et al (2021), Butler et al (2023)
SNFtool R package v2.3.1	https://cran.r‐project.org/web/packages/SNFtool/index.html (Wang et al, 2021)	N/A
stringi R package v1.7.6	https://cran.r‐project.org/web/packages/stringi/index.html	N/A
	Gagolewski & Tartanus (2023)
stringr R package v1.4.0	https://cran.r‐project.org/web/packages/stringr/index.html	N/A
	Wickham (2022b)
tidyr R package v1.2.0	https://cran.r‐project.org/web/packages/tidyr/index.html	N/A
	Wickham et al (2023c)