bioconductor projects | Ecosyste.ms: Papers

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: intansv

Integrative analysis of structural variations
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: MetaCyto

MetaCyto: A package for meta-analysis of cytometry data
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: InterMineR

R Interface with InterMine-Powered Databases
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: VanillaICE

A Hidden Markov Model for high throughput genotyping arrays
Papers that mentioned: 3

Likely Science (58)

bioconductor: dcanr

Differential co-expression/association network analysis
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: heatmaps

Flexible Heatmaps for Functional Genomics and Sequence Features
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: flowVS

Variance stabilization in flow cytometry (and microarrays)
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: iterativeBMA

The Iterative Bayesian Model Averaging (BMA) algorithm
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: HDF5Array

HDF5 backend for DelayedArray objects
Papers that mentioned: 3

Very Likely Science (90)

bioconductor: GSReg

Gene Set Regulation (GS-Reg)
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: MOGAMUN

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: msgbsR

msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: MPFE

Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
Papers that mentioned: 3

Very Likely Science (83)

bioconductor: switchBox

Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: hypeR

An R Package For Geneset Enrichment Workflows
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: flowCHIC

Analyze flow cytometric data using histogram information
Papers that mentioned: 3

Very Likely Science (90)

bioconductor: agilp

Agilent expression array processing package
Papers that mentioned: 3

Very Likely Science (93)

bioconductor: SubCellBarCode

SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome
Papers that mentioned: 3

Very Likely Science (90)

bioconductor: Nebulosa

Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: lmdme

Linear Model decomposition for Designed Multivariate Experiments
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: ngsReports

Load FastqQC reports and other NGS related files
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: NTW

Predict gene network using an Ordinary Differential Equation (ODE) based method
Papers that mentioned: 3

Very Likely Science (93)

bioconductor: FRASER

Find RAre Splicing Events in RNA-Seq Data
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: beadarraySNP

Normalization and reporting of Illumina SNP bead arrays
Papers that mentioned: 3

Very Likely Science (90)

bioconductor: cliqueMS

Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Papers that mentioned: 3

Very Likely Science (90)

bioconductor: splineTimeR

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: doppelgangR

Identify likely duplicate samples from genomic or meta-data
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: rexposome

Exposome exploration and outcome data analysis
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: oncomix

Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: SpeCond

Condition specific detection from expression data
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: OncoSimulR

Forward Genetic Simulation of Cancer Progression with Epistasis
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: zFPKM

A suite of functions to facilitate zFPKM transformations
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: OUTRIDER

OUTRIDER - OUTlier in RNA-Seq fInDER
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: ggmsa

Plot Multiple Sequence Alignment using 'ggplot2'
Papers that mentioned: 3

Very Likely Science (90)

bioconductor: panp

Presence-Absence Calls from Negative Strand Matching Probesets
Papers that mentioned: 3

Very Likely Science (75)

bioconductor: dStruct

Identifying differentially reactive regions from RNA structurome profiling data
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: VennDetail

A package for visualization and extract details
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: erccdashboard

Assess Differential Gene Expression Experiments with ERCC Controls
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: paxtoolsr

Access Pathways from Multiple Databases Through BioPAX and Pathway Commons
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: BubbleTree

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
Papers that mentioned: 3

Very Likely Science (70)

bioconductor: gep2pep

Creation and Analysis of Pathway Expression Profiles (PEPs)
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: BufferedMatrixMethods

Microarray Data related methods that utlize BufferedMatrix objects
Papers that mentioned: 3

Very Likely Science (85)

bioconductor: pepStat

Statistical analysis of peptide microarrays
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: CellMapper

Predict genes expressed selectively in specific cell types
Papers that mentioned: 3

Very Likely Science (95)

bioconductor: ChIPComp

Quantitative comparison of multiple ChIP-seq datasets
Papers that mentioned: 3

Very Likely Science (98)

bioconductor: DNABarcodes

A tool for creating and analysing DNA barcodes used in Next Generation Sequencing multiplexing experiments
Papers that mentioned: 3

Very Likely Science (100)

bioconductor: flowAI

Automatic and interactive quality control for flow cytometry data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: NoRCE

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: OLINgui

Graphical user interface for OLIN
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: pepXMLTab

Parsing pepXML files and filter based on peptide FDR.
Papers that mentioned: 2

Very Likely Science (98)

bioconductor: copa

Functions to perform cancer outlier profile analysis.
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: MultiMed

Testing multiple biological mediators simultaneously
Papers that mentioned: 2

Very Likely Science (98)

bioconductor: CONFESS

Cell OrderiNg by FluorEScence Signal
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: rain

Rhythmicity Analysis Incorporating Non-parametric Methods
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: Clonality

Clonality testing
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: ReQON

Recalibrating Quality Of Nucleotides
Papers that mentioned: 2

Very Likely Science (65)

bioconductor: CINdex

Chromosome Instability Index
Papers that mentioned: 2

Very Likely Science (73)

bioconductor: roar

Identify differential APA usage from RNA-seq alignments
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: CausalR

Causal network analysis methods
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: scBFA

A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: SCBN

A statistical normalization method and differential expression analysis for RNA-seq data between different species
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: BEARscc

BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
Papers that mentioned: 2

Very Likely Science (93)

bioconductor: scp

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: SemDist

Information Accretion-based Function Predictor Evaluation
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: seqbias

Estimation of per-position bias in high-throughput sequencing data
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: seqsetvis

Set Based Visualizations for Next-Gen Sequencing Data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: nethet

A bioconductor package for high-dimensional exploration of biological network heterogeneity
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: ANF

Affinity Network Fusion for Complex Patient Clustering
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: nondetects

Non-detects in qPCR data
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: XINA

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: Ularcirc

Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: VegaMC

VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
Papers that mentioned: 2

Likely Science (50)

bioconductor: zlibbioc

An R packaged zlib-1.2.5
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: Uniquorn

Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
Papers that mentioned: 2

Very Likely Science (65)

bioconductor: eudysbiome

Cartesian plot and contingency test on 16S Microbial data
Papers that mentioned: 2

Very Likely Science (83)

bioconductor: DepecheR

Determination of essential phenotypic elements of clusters in high-dimensional entities
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: TMixClust

Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: mpra

Analyze massively parallel reporter assays
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: msmsEDA

Exploratory Data Analysis of LC-MS/MS data by spectral counts
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: msPurity

Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics
Papers that mentioned: 2

Very Likely Science (100)

bioconductor projects 1,374