Package: decoupleR 2.11.0

Pau Badia-i-Mompel

decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data

Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present decoupleR, a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

Authors:Pau Badia-i-Mompel [aut, cre], Jesús Vélez-Santiago [aut], Jana Braunger [aut], Celina Geiss [aut], Daniel Dimitrov [aut], Sophia Müller-Dott [aut], Petr Taus [aut], Aurélien Dugourd [aut], Christian H. Holland [aut], Ricardo O. Ramirez Flores [aut], Julio Saez-Rodriguez [aut]

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NEWS

# Install 'decoupleR' in R:

install.packages('decoupleR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/saezlab/decoupler/issues

On BioConductor:decoupleR-2.11.0(bioc 3.20)decoupleR-2.10.0(bioc 3.19)

bioconductor-package

43 exports 2.09 score 34 dependencies 3 dependents

Last updated 2 months agofrom:aa9e0db72e

Exports::=.data .fit_preprocessing %>%abort as_label as_name check_corr convert_f_defaults decouple enquo enquos exec expr extract_sets filt_minsize get_collectri get_dorothea get_ksn_omnipath get_progeny get_resource get_toy_data intersect_regulons pivot_wider_profile quo_is_missing quo_is_null rename_net run_aucell run_consensus run_fgsea run_gsva run_mdt run_mlm run_ora run_udt run_ulm run_viper run_wmean run_wsum show_methods show_resources sym syms

Dependencies:backports BH BiocParallel broom cli codetools cpp11 dplyr fansi formatR futile.logger futile.options generics glue lambda.r lattice lifecycle magrittr Matrix parallelly pillar pkgconfig purrr R6 rlang snow stringi stringr tibble tidyr tidyselect utf8 vctrs withr

Introduction

Pau Badia-i-Mompel, Jesús Vélez-Santiago

Rendered fromdecoupleR.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-04-01
Started: 2020-12-14

Pathway activity inference from scRNA-seq

Pau Badia-i-Mompel

Rendered frompw_sc.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-21
Started: 2022-03-30

Pathway activity inference in bulk RNA-seq

Pau Badia-i-Mompel

Rendered frompw_bk.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-21
Started: 2022-04-01

Transcription factor activity inference from scRNA-seq

Pau Badia-i-Mompel

Rendered fromtf_sc.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-21
Started: 2022-03-30

Transcription factor activity inference in bulk RNA-seq

Pau Badia-i-Mompel

Rendered fromtf_bk.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-11-21
Started: 2022-04-01

Help page	Topics
Pre-processing for methods that fit networks.	.fit_preprocessing
Check correlation (colinearity)	check_corr
Rename columns and add defaults values if column not present	convert_f_defaults
Evaluate multiple statistics with same input data	decouple
Extract sets	extract_sets
Filter sources with minsize targets	filt_minsize
CollecTRI gene regulatory network. Wrapper to access CollecTRI gene regulatory network. CollecTRI is a comprehensive resource containing a curated collection of transcription factors (TFs) and their target genes. It is an expansion of DoRothEA. Each interaction is weighted by its mode of regulation (either positive or negative).	get_collectri
DoRothEA gene regulatory network.	get_dorothea
OmniPath kinase-substrate network	get_ksn_omnipath
Pathway RespOnsive GENes for activity inference (PROGENy).	get_progeny
Wrapper to access resources inside Omnipath. This wrapper allows to easily query different prior knowledge resources. To check available resources run 'decoupleR::show_resources()'. For more information visit the official website for Omnipath.	get_resource
Generate a toy 'mat' and 'network'.	get_toy_data
Intersect network target features with input matrix.	intersect_regulons
Rename network	rename_net
AUCell	run_aucell
Consensus score between methods	run_consensus
Fast Gene Set Enrichment Analysis (FGSEA)	run_fgsea
Gene Set Variation Analysis (GSVA)	run_gsva
Multivariate Decision Trees (MDT)	run_mdt
Multivariate Linear Model (MLM)	run_mlm
Over Representation Analysis (ORA)	run_ora
Univariate Decision Tree (UDT)	run_udt
Univariate Linear Model (ULM)	run_ulm
Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER)	run_viper
Weighted Mean (WMEAN)	run_wmean
Weighted Sum (WSUM)	run_wsum
Show methods	show_methods
Shows available resources in Omnipath. For more information visit the official website for Omnipath.	show_resources

Package: decoupleR 2.11.0

decoupleR: decoupleR: Ensemble of computational methods to infer biological activities from omics data

Introduction

Pathway activity inference from scRNA-seq

Pathway activity inference in bulk RNA-seq

Transcription factor activity inference from scRNA-seq

Transcription factor activity inference in bulk RNA-seq

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)