bioconductor projects | Ecosyste.ms: Papers

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Papers that mentioned: 5

Very Likely Science (83)

bioconductor: EMDomics

Earth Mover's Distance for Differential Analysis of Genomics Data
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: mgsa

Model-based gene set analysis
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: gaggle

Broadcast data between R and Gaggle
Papers that mentioned: 5

Very Likely Science (90)

bioconductor: Guitar

Guitar
Papers that mentioned: 5

Very Likely Science (98)

bioconductor: hpar

Human Protein Atlas in R
Papers that mentioned: 5

Very Likely Science (90)

bioconductor: iCheck

QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: LBE

Estimation of the false discovery rate.
Papers that mentioned: 5

Very Likely Science (75)

bioconductor: MAGeCKFlute

Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: MethPed

A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
Papers that mentioned: 5

Very Likely Science (95)

bioconductor: MGFM

Marker Gene Finder in Microarray gene expression data
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: motifmatchr

Fast Motif Matching in R
Papers that mentioned: 5

Likely Science (50)

bioconductor: MSstatsTMT

Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: PREDA

Position Related Data Analysis
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: R4RNA

An R package for RNA visualization and analysis
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: sangeranalyseR

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: UNDO

Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
Papers that mentioned: 5

Very Likely Science (93)

bioconductor: affyio

Tools for parsing Affymetrix data files
Papers that mentioned: 5

Very Likely Science (100)

High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)
Papers that mentioned: 5

Very Likely Science (90)

bioconductor: EBcoexpress

EBcoexpress for Differential Co-Expression Analysis
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: EventPointer

An effective identification of alternative splicing events using junction arrays and RNA-Seq data
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: genomeIntervals

Operations on genomic intervals
Papers that mentioned: 5

Very Likely Science (90)

bioconductor: LOBSTAHS

Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Papers that mentioned: 5

Very Likely Science (74)

bioconductor: MetID

Network-based prioritization of putative metabolite IDs
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: pwrEWAS

A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
Papers that mentioned: 5

Very Likely Science (98)

bioconductor: RITAN

Rapid Integration of Term Annotation and Network resources
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: SpacePAC

Identification of Mutational Clusters in 3D Protein Space via Simulation.
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: TargetScore

TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
Papers that mentioned: 5

Very Likely Science (93)

bioconductor: MultiDataSet

Implementation of MultiDataSet and ResultSet
Papers that mentioned: 5

Very Likely Science (75)

bioconductor: omicsPrint

Cross omic genetic fingerprinting
Papers that mentioned: 5

Very Likely Science (75)

bioconductor: PhyloProfile

PhyloProfile
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: annmap

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: bamsignals

Extract read count signals from bam files
Papers that mentioned: 5

Very Likely Science (95)

bioconductor: ChIPseqR

Identifying Protein Binding Sites in High-Throughput Sequencing Data
Papers that mentioned: 5

Very Likely Science (60)

bioconductor: scone

Single Cell Overview of Normalized Expression data
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: segmentSeq

Methods for identifying small RNA loci from high-throughput sequencing data
Papers that mentioned: 5

Very Likely Science (83)

bioconductor: Cormotif

Correlation Motif Fit
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: ctc

Cluster and Tree Conversion.
Papers that mentioned: 5

Very Likely Science (90)

bioconductor: DAPAR

Tools for the Differential Analysis of Proteins Abundance with R
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: SpectralTAD

SpectralTAD: Hierarchical TAD detection using spectral clustering
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: ssize

Estimate Microarray Sample Size
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: switchde

Switch-like differential expression across single-cell trajectories
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: TitanCNA

Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: YAPSA

Yet Another Package for Signature Analysis
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: GraphPAC

Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.
Papers that mentioned: 5

Very Likely Science (98)

bioconductor: GRridge

Better prediction by use of co-data: Adaptive group-regularized ridge regression
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: gtrellis

Genome Level Trellis Layout
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: CNORode

ODE add-on to CellNOptR
Papers that mentioned: 5

Very Likely Science (90)

bioconductor: AMARETTO

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
Papers that mentioned: 5

Very Likely Science (70)

bioconductor: altcdfenvs

alternative CDF environments (aka probeset mappings)
Papers that mentioned: 5

Very Likely Science (60)

bioconductor: gpls

Classification using generalized partial least squares
Papers that mentioned: 5

Very Likely Science (90)

bioconductor: atSNP

Affinity test for identifying regulatory SNPs
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: CRImage

CRImage a package to classify cells and calculate tumour cellularity
Papers that mentioned: 5

Very Likely Science (90)

bioconductor: funtooNorm

Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Papers that mentioned: 5

Very Likely Science (75)

bioconductor: MPRAnalyze

Statistical Analysis of MPRA data
Papers that mentioned: 5

Very Likely Science (100)

bioconductor: RandomWalkRestartMH

Random walk with restart on multiplex and heterogeneous Networks
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: ddCt

The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: MOSim

Multi-Omics Simulation (MOSim)
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: aroma.light

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: BiGGR

Constraint based modeling in R using metabolic reconstruction databases
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: MSPrep

Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: ABarray

Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
Papers that mentioned: 4

Very Likely Science (75)

bioconductor: miRmine

Data package with miRNA-seq datasets from miRmine database as RangedSummarizedExperiment
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: RareVariantVis

A suite for analysis of rare genomic variants in whole genome sequencing data
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: APAlyzer

A toolkit for APA analysis using RNA-seq data
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: flowCL

Papers that mentioned: 4

Unlikely Science (0)

bioconductor: GOexpress

Visualise microarray and RNAseq data using gene ontology annotations
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: BioNetStat

Biological Network Analysis
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: GUIDEseq

GUIDE-seq and PEtag-seq analysis pipeline
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: BADER

Bayesian Analysis of Differential Expression in RNA Sequencing Data
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: statTarget

Statistical Analysis of Molecular Profiles
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: scAlign

Papers that mentioned: 4

Unlikely Science (0)

bioconductor: muscat

Multi-sample multi-group scRNA-seq data analysis tools
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: esATAC

An Easy-to-use Systematic pipeline for ATACseq data analysis
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: mzID

An mzIdentML parser for R
Papers that mentioned: 4

Very Likely Science (90)

bioconductor: NanoStringQCPro

Quality metrics and data processing methods for NanoString mRNA gene expression data
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: GRmetrics

Calculate growth-rate inhibition (GR) metrics
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: msmsTests

LC-MS/MS Differential Expression Tests
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: GraphAlignment

GraphAlignment
Papers that mentioned: 4

Very Likely Science (90)

bioconductor: ChemmineOB

R interface to a subset of OpenBabel functionalities
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: HybridMTest

Hybrid Multiple Testing
Papers that mentioned: 4

Very Likely Science (90)

bioconductor: pdInfoBuilder

Platform Design Information Package Builder
Papers that mentioned: 4

Very Likely Science (75)

bioconductor: casper

Characterization of Alternative Splicing based on Paired-End Reads
Papers that mentioned: 4

Very Likely Science (90)

bioconductor: SCATE

SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: mBPCR

Bayesian Piecewise Constant Regression for DNA copy number estimation
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: SeqVarTools

Tools for variant data
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: cellTree

Papers that mentioned: 4

Unlikely Science (0)

bioconductor: BUS

Gene network reconstruction
Papers that mentioned: 4

Very Likely Science (93)

bioconductor: bacon

Controlling bias and inflation in association studies using the empirical null distribution
Papers that mentioned: 4

Very Likely Science (90)

bioconductor: ASpli

Analysis of Alternative Splicing Using RNA-Seq
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: BridgeDbR

Code for using BridgeDb identifier mapping framework from within R
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: BHC

Bayesian Hierarchical Clustering
Papers that mentioned: 4

Very Likely Science (100)

bioconductor: DegNorm

DegNorm: degradation normalization for RNA-seq data
Papers that mentioned: 4

Very Likely Science (100)

bioconductor projects 1,374