ARTNet Moonshot Software Sharing Catalog

Name	Description	Latest Version	Contact	License	Keywords	Consortium
5-UTR-Mutation-Analysis	5′-UTR cis-regulatory element mutation analysis	1.0.0	Andrew C. Hsieh	-	5′-UTR; Cis-Regulatory Element; Mutation Analysis	DRSN
AMLResistanceNetworks	Proteomic and phosphoproteomic measurements enhance ability to predict ex vivo drug response in AML	0.1	Karin Rodland	MIT	AML; Drug Response; Drug Sensitivity	ARTNet
antigen-combos-scripts	In silico Screening of Antigen Combinations	-	Wendell A. Lim	Clear BSD	Computational Reproducibility; Neoantigen	IOTN
BayesNetBP	Bayesian Network Belief Propagation	1.5.5	Han Yu	GPL-3	Statistics; Graphics Visualization; Causal Network	IOTN; DRSN
beatAML2	Integrative Analysis of Drug Response and Clinical Outcome in Acute Myeloid Leukemia	1.0.0	Jeffrey W Tyner	-	Workflow; Computational Reproducibility	ARTNet
beatAMLproteomics	Proteomic and phosphoproteomic measurements enhance ability to predict ex vivo drug response in AML	-	Karin Rodland	MIT	Workflow; Computational Reproducibility	ARTNet
CART19_intsite	CD19-targeting CAR T cell immunotherapy outcomes correlate with genomic modification by vector integration	v0.9.2	J Joseph Melenhorst	GPL-3	Computational Reproducibility; Vector-Integration Sites	IOTN
Cerebra	Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing	1.2.0	Lincoln Harris	MIT	Variant Summary; Variant Interpretation; Variant Calling Format (VCF)	DRSN
comut	A Python library for visualizing genomic and phenotypic information via comutation plots	0.0.3	Eliezer M. Van Allen	MIT	Graphics Visualization	IOTN
COVID19ELLA	An inflammatory cytokine signature predicts COVID-19 severity and survival	-	Sacha Gnjatic	-	Computational Reproducibility; Gene Signature	IOTN
DARTS	Deep-learning Augmented RNA-seq Analysis of Transcript Splicing	0.1.0	Yi Xing	-	Deep-learning; RNA Splicing	IOTN
FARDEEP	A new machine learning tool for enumerating immune cell subsets from whole tumor tissue samples.	-	Yu Leo Lei	-	Computational Reproducibility; Cell Composition Deconvolution	IOTN
GoPeaks	Histone modification peak calling for CUT&Tag	1.0.0	Theodore Braun	MIT	Peak-calling; CUT&TAG/CUT&RUN; Narrow Peaks	ARTNet
GoPeaks-compare	Histone modification peak calling for CUT&Tag	-	Theodore Braun	MIT	Workflow; Computational Reproducibility	ARTNet
HitWalker2	Visual analytics for precision medicine and beyond	1	Shannon K. McWeeney	MIT	Prioritization; Visualization; Network; Precision Medicine	DRSN
HMMRATAC	The Hidden Markov Modeler for ATAC-seq	1.2.10	Tao Liu	GPL-3	ATAC-seq; Peak-calling	DRSN; IOTN
Lim-5utr-Paper-code	Multiplexed functional genomic analysis of 5' untranslated region mutations across the spectrum of prostate cancer	1.0.0	Andrew C. Hsieh	-	Computational Reproducibility	DRSN
MAESTRO	Model-based AnalysEs of Single-cell Transcriptome and RegulOme	1.3.2	Tao Liu	GPL-3	Single-cell ATAC-seq Analysis; Single-cell RNA-seq Analysis; Integrative Pipeline	IOTN; DRSN
metaBLUE	BLUE for Combining Location and Scale Information in a Meta-Analysis	1.0.0	Alan Hutson	GPL-2	Statistics	IOTN; DRSN
MetaPhOR	Metabolic Pathway Analysis of RNA	1.0.0	Spencer Rosario	Artistic-2.0	Transcription; Metabolism; Bioconductor; Pathway Enrichment	ARTNet; CAP-IT
Molecular Oncology Almanac portal	A cloud-based web portal for accessible clinical interpretation of integrative cancer genomics.	-	Eliezer M. Van Allen	Apache License 2.0	Integrative Analysis; Web portal	IOTN
OSCA-BIOC	Orchestrating single-cell analysis with Bioconductor	1.0.6	Stephanie C. Hicks	CC BY-NC-ND 3.0 US	Single-cell RNA-seq Analysis; Bioconductor	DRSN; IOTN
PEGASAS	Pathway Enrichment-Guided Activity Study of Alternative Splicing	1.1.0	Yi Xing	-	RNA Splicing	IOTN
PEGASAS-Figure-Scripts	Pathway-guided Analysis Identifies Myc-dependent Alternative pre-mRNA Splicing in Aggressive Prostate Cancers	-	Yi Xing	-	Computational Reproducibility; RNA Splicing	IOTN
perk	Robust permutation tests of correlation coefficients	0.1.0	Han Yu	GPL-3	Statistics	IOTN
QuantileNPCI	Calculating nonparametric confidence intervals for quantiles using fractional order statistics	0.9.0	Li Yan	GPL-3	Statistics	IOTN
quantsig	Sigmoidal Quantile Function Estimator	0.1.0	Han Yu	GPL-3	Statistics	ARTNet
Rcwl	An R interface to the Common Workflow Language	1.7.12	Qian Liu	GPL-2	Workflow	IOTN; DRSN
RcwlPipelines	A collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.	1.7.7	Qian Liu	GPL-2	DNA-seq Analysis; RNA-seq Analysis; Data import; Quality Control; Workflow	DRSN; IOTN
ReactomeFIViz	Reactome FI Cytoscape app for use with Cytoscape version 3.0.0 and later	7.2.3	Guanming Wu	-	Visualization; Pathway Analysis; Network	DRSN
rMATS turbo	A C/Cython version of rMATS to detect differential alternative splicing events from RNA-Seq data	4.1.1	Yi Xing	2-Clause BSD	RNA Splicing	IOTN
scell_lung_adenocarcinoma	Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing	-	Trever G Bivona	-	Computational Reproducibility; Single-cell RNA-seq Analysis	DRSN
schadendorf-pd1	Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma	-	Eliezer M. Van Allen	GPL-3	Computational Reproducibility; Integrative Analysis	IOTN
ScreenProcessing	GATOR2-dependent mTORC1 activity is a therapeutic vulnerability in FOXO1 fusion–positive rhabdomyosarcoma	0.2	Amit J Sabnis	-	Workflow; Computational Reproducibility	ARTNet
Vizome	Vizome: The online data browser for functional genomics datasets of AML	-	Shannon K. McWeeney	-	Data Browser	DRSN

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IOTN Software Sharing Catalog