Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: cran: MultiAssayExperiment

View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/MultiAssayExperiment

Dependent Repos 78

microbiome/mia
Microbiome analysis
  • * DESCRIPTION

Size: 21.1 MB - Last synced: 20 days ago - Pushed: 20 days ago

insightsengineering/teal.slice
Reproducible slice module for teal applications
  • * DESCRIPTION

Size: 55.7 MB - Last synced: about 6 hours ago - Pushed: 1 day ago

insightsengineering/teal.data
Data model for teal applications
  • * DESCRIPTION

Size: 29.5 MB - Last synced: 21 days ago - Pushed: 22 days ago

bhklab/PharmacoGx
R package to analyze large-scale pharmacogenomic datasets.
  • * DESCRIPTION

Size: 70.8 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

insightsengineering/hermes
Preprocessing, analyzing, and reporting of RNA-seq data
  • * DESCRIPTION

Size: 45.2 MB - Last synced: 13 days ago - Pushed: about 1 month ago

Syksy/curatedPCaData
Bioconductor R-package: Curated Prostate Cancer Data
  • * DESCRIPTION

Size: 4.49 MB - Last synced: 14 days ago - Pushed: 15 days ago

insightsengineering/teal.modules.hermes
RNA-seq analysis modules to add to a teal application
  • * DESCRIPTION

Size: 19 MB - Last synced: 2 days ago - Pushed: 2 days ago

bioFAM/MOFA2
Multi-Omics Factor Analysis
  • * DESCRIPTION

Size: 162 MB - Last synced: 2 days ago - Pushed: 5 months ago

rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data
  • * DESCRIPTION

Size: 21.4 MB - Last synced: 29 days ago - Pushed: 30 days ago

HelenLindsay/AbNames
Standardize antibody names and match to genes
  • * DESCRIPTION

Size: 42.1 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

waldronlab/curatedTCGAData
Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
  • * DESCRIPTION

Size: 2.26 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

kokonech/InTAD
Correlation of epigenetic signals and genes in TADs/via loops
  • * DESCRIPTION

Size: 517 KB - Last synced: 8 months ago - Pushed: over 2 years ago

BaderLab/netDx
R package with netDx software and data for examples
  • * DESCRIPTION

Size: 115 MB - Last synced: 3 months ago - Pushed: over 1 year ago

bhklab/bioc2022workshop
A workshop on drug combination experiment support in CoreGx and PharmacoGx.
  • * DESCRIPTION

Size: 143 MB - Last synced: 2 months ago - Pushed: about 1 year ago

waldronlab/cBioPortalData
Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
  • * DESCRIPTION

Size: 2.01 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

bkaczkowski/xcore
  • >= 1.18.0 DESCRIPTION

Size: 7.93 MB - Last synced: 6 months ago - Pushed: 6 months ago

Huber-group-EMBL/mofaCLL
  • * DESCRIPTION

Size: 108 MB - Last synced: 3 months ago - Pushed: 3 months ago

neobernad/evaluomeR
The evaluomeR package is an R package which permits to evaluate the reliability of bioinformatic metrics.
  • * DESCRIPTION

Size: 29.6 MB - Last synced: 1 day ago - Pushed: 2 days ago

bhagwataditya/autonomics
  • * DESCRIPTION

Size: 13 MB - Last synced: 5 days ago - Pushed: 5 days ago

gevaertlab/AMARETTO
Regulatory network inference and driver gene evaluation using integrative multi-omics analysis and penalized regression
  • * DESCRIPTION

Size: 78 MB - Last synced: 8 months ago - Pushed: about 1 year ago

computational-metabolomics/metabolomicsWorkbenchR
R/Bioconductor Package - Interface to the Metabolomics Workbench RESTful API
  • * DESCRIPTION

Size: 5.01 MB - Last synced: 9 months ago - Pushed: 9 months ago

isglobal-brge/MultiDataSet
Bioconductor package to encapsulate multiple datasets (including BioC omic data types)
  • * DESCRIPTION

Size: 595 KB - Last synced: 3 months ago - Pushed: over 2 years ago

sysbiomed/glmSparseNet
An R :package: for network-based and sparse generalized linear models (GLM)
  • * DESCRIPTION

Size: 16.9 MB - Last synced: about 1 month ago - Pushed: 4 months ago

Genentech/midasHLA
R package enabling statistical association analysis and using immunogenetic data transformation functions for HLA amino acid fine mapping, analysis of HLA evolutionary divergence as well as HLA-KIR interactions.
  • >= 1.8.3 DESCRIPTION

Size: 13.3 MB - Last synced: 3 months ago - Pushed: 4 months ago

lgatto/QFeaturesWorkshop2020
QFeatures: Quantitative features for mass spectrometry data
  • * DESCRIPTION

Size: 1.37 MB - Last synced: over 1 year ago - Pushed: over 3 years ago

Bioconductor/RaggedExperiment
Matrix-like representations of mutation and CN data
  • * DESCRIPTION

Size: 202 KB - Last synced: about 1 month ago - Pushed: about 1 month ago

isglobal-brge/brge_data_large
Compendium of packages used in BRGE group
  • * DESCRIPTION

Size: 5.22 GB - Last synced: 11 months ago - Pushed: 11 months ago

r-pkg-team/r-bioc-mofa
Multi-Omics Factor Analysis (MOFA)
  • * DESCRIPTION

Last synced: over 1 year ago

facilebio/FacileBiocData
Implements the FacileData API over standard bioconductor assay containers
  • * DESCRIPTION

Size: 650 KB - Last synced: about 1 month ago - Pushed: 9 months ago

insightsengineering/teal
Exploratory Web Apps for Analyzing Clinical Trial Data
  • * DESCRIPTION

Size: 43.7 MB - Last synced: 5 months ago - Pushed: 5 months ago

charles-plessy/CAGEr
Mirror of Bioconductor's CAGEr package repository
  • * DESCRIPTION

Size: 7.48 MB - Last synced: about 4 hours ago - Pushed: about 10 hours ago

fjcamlab/deco
DECO :: Decomposing heterogeneous population cohorts for patient stratification and discovery of biomarkers using omic data profiling. R package
  • * DESCRIPTION

Size: 16.9 MB - Last synced: about 2 months ago - Pushed: over 2 years ago

microbiome/microbiomeDataSets
Experiment Hub based microbiome datasets
  • * DESCRIPTION

Size: 14.5 MB - Last synced: 3 months ago - Pushed: almost 2 years ago

bhklab/PDATK
  • * DESCRIPTION

Size: 35.2 MB - Last synced: 2 months ago - Pushed: over 2 years ago

waldronlab/SingleCellMultiModal
Single Cell multimodal data scripts for downloading datasets
  • * DESCRIPTION

Size: 733 KB - Last synced: about 1 month ago - Pushed: about 1 month ago

DarioS/ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
  • >= 1.6.0 DESCRIPTION

Size: 12.2 MB - Last synced: 3 days ago - Pushed: 3 days ago

iloveless1/EpiXprS
Methods for associating DNA methylation with gene expression in a multivariate context. One can similarly assess the role of any potential dichotomous modifier in this relationship.
  • * DESCRIPTION

Size: 18.4 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

wejlab/curatedTBData
Curation of existing TB gene expression datasets
  • * DESCRIPTION

Size: 1.44 MB - Last synced: 21 days ago - Pushed: 3 months ago

aljabadi/BIRSBIO2020.scNMTseq.PLS
BIRS Bio-integration 2020 scNMTseq challenge analysis using PLS approach
  • * DESCRIPTION

Size: 25.5 MB - Last synced: 11 months ago - Pushed: about 3 years ago

lgatto/QFeaturesScpWorkshop2021
QFeatures and scp Bioc2021 workshop
  • * DESCRIPTION

Size: 175 MB - Last synced: 4 months ago - Pushed: almost 3 years ago

waldronlab/MicrobiomeWorkshop
A workshop on microbiome analysis using Bioconductor
  • * DESCRIPTION

Size: 13.3 MB - Last synced: about 2 months ago - Pushed: almost 5 years ago

wejlab/MetaScope
An R-based approach for preprocessing and aligning 16S, metagenomic, and metatranscriptomic data (PathoScope version 3.0)
  • * DESCRIPTION

Size: 30.2 MB - Last synced: 21 days ago - Pushed: about 1 month ago

jw156605/BIRSBIO2020.scNMTseq.LIGER
BIRSBIO2020 workshop, scNMTseq data, LIGER analysis
  • * DESCRIPTION

Size: 879 KB - Last synced: over 1 year ago - Pushed: almost 3 years ago

UCLouvain-CBIO/scp
Single cell proteomics data processing
  • * DESCRIPTION

Size: 64.2 MB - Last synced: 2 months ago - Pushed: 2 months ago

waldronlab/CNVRanger
Functionality for CNV analysis
  • * DESCRIPTION

Size: 15.9 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

martahidalgo/hipathia
Hipathia is a package for Signaling pathway analysis and Signaling pathway functional analysis.
  • >= 1.4.9 DESCRIPTION

Size: 150 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

wejlab/animalcules
R shiny app for interactive microbiome analysis
  • * DESCRIPTION

Size: 18.6 MB - Last synced: 22 days ago - Pushed: 4 months ago

r-pkg-team/r-bioc-mofa2
Multi-Omics Factor Analysis v2
  • * DESCRIPTION

Last synced: over 1 year ago

ChangqingW/FLAMES-R Fork of mritchielab/FLAMES
  • * DESCRIPTION

Size: 87.6 MB - Last synced: 2 months ago - Pushed: 2 months ago

philyang07/scPipe Fork of shaniAmare/scPipe
a pipeline for single cell RNA-seq data analysis
  • * DESCRIPTION

Size: 156 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

vjcitn/BiocOncoTK
Bioconductor components for general cancer genomics
  • * DESCRIPTION

Size: 15.2 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

waldronlab/TCGAutils
Toolbox package for organizing and working with TCGA data
  • * DESCRIPTION

Size: 753 KB - Last synced: about 1 month ago - Pushed: about 1 month ago

kokonech/intad
  • * DESCRIPTION

Size: 1.86 MB - Last synced: over 1 year ago

IFB-ElixirFr/ProMetIS
  • * DESCRIPTION

Size: 256 MB - Last synced: 27 days ago - Pushed: 28 days ago

laurenhsu1/corral
Dimensionality reduction and batch integration methods for single cell data
  • * DESCRIPTION

Size: 1.36 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

bioFAM/MOFA
Multi-Omics Factor Analysis
  • * DESCRIPTION

Size: 116 MB - Last synced: 1 day ago - Pushed: over 3 years ago

ConesaLab/multibac
  • * DESCRIPTION

Size: 616 KB - Last synced: over 1 year ago

graumannlabtools/autonomics
  • * DESCRIPTION

Size: 108 MB - Last synced: over 1 year ago

josefcatala/paquete_tfmjf
Paquete con funciones para los análisis del Trabajo Fin de Master
  • * DESCRIPTION

Last synced: about 1 year ago

ahopki14/RepertoireExperiment
Defines an R S4 object for T and B cell receptor repertoire data.
  • * DESCRIPTION

Last synced: over 1 year ago

PoisonAlien/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  • * DESCRIPTION

Size: 72.3 MB - Last synced: 14 days ago - Pushed: 14 days ago

SydneyBioX/ClassifyR Fork of DarioS/ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
  • * DESCRIPTION

Size: 12.2 MB - Last synced: 3 days ago - Pushed: 3 days ago

shaniAmare/scPipe Fork of LuyiTian/scPipe
a pipeline for single cell data analysis
  • * DESCRIPTION

Size: 156 MB - Last synced: 8 months ago - Pushed: 8 months ago

OliverVoogd/scPipe Fork of shaniAmare/scPipe
a pipeline for single cell RNA-seq data analysis
  • * DESCRIPTION

Size: 156 MB - Last synced: 8 months ago - Pushed: 8 months ago

cvanderaa/QFeatures Fork of rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data
  • * DESCRIPTION

Size: 16.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

waldronlab/MultiAssayWorkshop
Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment
  • * DESCRIPTION

Size: 2.78 MB - Last synced: 6 months ago - Pushed: 6 months ago

bioFAM/MOFAdata
Data for Multi-Omics Factor Analysis (MOFA)
  • * DESCRIPTION

Size: 118 MB - Last synced: 1 day ago - Pushed: about 1 year ago

samWieczorek/old_DaparToolshed
  • * DESCRIPTION

Size: 26.9 MB - Last synced: 8 months ago - Pushed: 8 months ago

isglobal-brge/brge.omic
Collection of BRGE omic data encapsulated in stardard R structures
  • * DESCRIPTION

Size: 125 MB - Last synced: 5 months ago - Pushed: over 6 years ago

MTurner0/maeplyr
"maeplyr" is an R package providing dplyr-like tools for manipulation of MultiAssayExperiment and SummarizedExperiment objects.
  • * DESCRIPTION

Size: 2.55 MB - Last synced: about 15 hours ago - Pushed: over 1 year ago

waldronlab/PublicDataResources
Public data resources and Bioconductor: The goal of this workshop is to introduce Bioconductor packages for finding, accessing, and using large-scale public data resources including the Gene Expression Omnibus GEO, Sequence Read Archive SRA, the Genomic Data Commons GDC, and Bioconductor-hosted curated data resources for metagenomics, pharmacogenomics PharmacoDB, and The Cancer Genome Atlas.
  • * DESCRIPTION

Size: 3.29 MB - Last synced: 8 months ago - Pushed: about 3 years ago

giupardeb/EpiMethEx
EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between methylation and gene expression data.
  • * DESCRIPTION

Size: 227 KB - Last synced: 8 months ago - Pushed: over 5 years ago

molepi/omicsPrint
Cross omic genetic fingerprinting
  • * DESCRIPTION

Size: 25.4 MB - Last synced: 8 months ago - Pushed: over 5 years ago

babelomics/hipathia
Signaling pathway model
  • >= 1.4.9 DESCRIPTION

Size: 149 MB - Last synced: 8 months ago - Pushed: almost 2 years ago

mi2-warsaw/GOpro
  • * DESCRIPTION

Size: 1.73 MB - Last synced: 23 days ago - Pushed: over 7 years ago

icebert/CAGEr
fork of https://bioconductor.org/packages/CAGEr/
  • * DESCRIPTION

Size: 1.52 MB - Last synced: over 1 year ago - Pushed: over 1 year ago

ConesaLab/MultiBaC
Single and multiomic batch effect correction
  • * DESCRIPTION

Size: 5.75 MB - Last synced: 1 day ago - Pushed: over 2 years ago

facilebio/FacileTcgaDataSet
Assembles a pan-indication, multi-assay TCGA FacileDataSet
  • * DESCRIPTION

Size: 66.4 KB - Last synced: over 1 year ago - Pushed: almost 5 years ago

glin/brgedata
  • * DESCRIPTION

Size: 1.69 GB - Last synced: over 1 year ago - Pushed: over 3 years ago

lpantano/bcbioSmallRna
R package to analyze data after small RNAseq with bcbio
  • * DESCRIPTION

Size: 17.7 MB - Last synced: 29 days ago - Pushed: over 4 years ago

tetomonti/SSML
Semi-Supervised Machine Learning Methods for Bioconductor
  • * DESCRIPTION

Size: 431 MB - Last synced: about 1 year ago - Pushed: about 5 years ago

cran/MOCHA
:exclamation: This is a read-only mirror of the CRAN R package repository. MOCHA — Modeling for Single-Cell Open Chromatin Analysis
  • * DESCRIPTION

Size: 4.5 MB - Last synced: 5 months ago - Pushed: 5 months ago

annalisaxamin/LBDM
Project for the course of Laboratory of Biological Data Mining
  • * R_code/CAGEr/DESCRIPTION

Size: 115 MB - Last synced: 9 months ago - Pushed: about 1 year ago

PreCanMed-KI/MOFA2_DHR
  • * MOFA2/DESCRIPTION

Size: 108 MB - Last synced: 3 months ago - Pushed: over 2 years ago

vjcitn/ogttMetrics
R package for managing and analyzing large collections of oral glucose tolerance tests
  • >= 1.1.49 DESCRIPTION

Size: 117 KB - Last synced: about 1 month ago - Pushed: about 7 years ago

vjcitn/brcaProteo
A package that illustrates use of CPTAC data on breast cancer in a multiomic context
  • * DESCRIPTION

Size: 10.3 MB - Last synced: about 1 month ago - Pushed: about 5 years ago

prostarproteomics/DaparToolshed
  • * DESCRIPTION

Size: 30.5 MB - Last synced: 1 day ago - Pushed: 1 day ago

isglobal-brge/brgedata
  • * DESCRIPTION

Size: 285 MB - Last synced: over 1 year ago - Pushed: almost 3 years ago

sa-lee/plyexperiment
A fluent interface to SummarizedExperiment
  • * DESCRIPTION

Size: 11.7 KB - Last synced: over 1 year ago - Pushed: over 5 years ago

LiNk-NY/curatedTCGAManu
Multi-omic integration of public oncology databases in Bioconductor
  • * DESCRIPTION

Size: 87.1 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

waldronlab/MultiAssayExperiment.TCGA
  • * DESCRIPTION

Size: 572 KB - Last synced: about 1 month ago - Pushed: about 1 year ago

LiNk-NY/MultiAssayExtra
  • * DESCRIPTION

Size: 3.91 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago

califano-lab/MOMA
  • * DESCRIPTION

Size: 221 MB - Last synced: 6 months ago - Pushed: about 3 years ago

BioinfOMICS/cBioPortalData Fork of waldronlab/cBioPortalData
Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
  • * DESCRIPTION

Size: 1.63 MB - Last synced: 11 months ago - Pushed: over 1 year ago

ruiatelsevier/MOFA2 Fork of bioFAM/MOFA2
Multi-Omics Factor Analysis V2 (MOFA+)
  • * DESCRIPTION

Size: 161 MB - Last synced: 11 months ago - Pushed: almost 3 years ago

ruiatelsevier/MOFAdata Fork of bioFAM/MOFAdata
Data for Multi-Omics Factor Analysis (MOFA)
  • * DESCRIPTION

Size: 118 MB - Last synced: 11 months ago - Pushed: almost 3 years ago

ashley-brooke/CSHstats Fork of vjcitn/CSHstats
R vignettes/pkgdown for elementary statistics for a summer course
  • * DESCRIPTION

Size: 11 MB - Last synced: 11 months ago - Pushed: almost 2 years ago

ashley-brooke/BiocWorkshops Fork of Bioconductor/BiocWorkshops
:warning: 2018 :warning: Bioconductor Workshops
  • * DESCRIPTION

Size: 137 MB - Last synced: 11 months ago - Pushed: about 5 years ago

GenomicsNX/MultiAssayWorkshop Fork of waldronlab/MultiAssayWorkshop
Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment
  • * DESCRIPTION

Size: 1.98 MB - Last synced: 2 months ago - Pushed: almost 3 years ago

GenomicsNX/maftools Fork of PoisonAlien/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  • * DESCRIPTION

Size: 63.4 MB - Last synced: 2 months ago - Pushed: almost 2 years ago