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
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
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
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
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
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
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
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