bioconductor projects | Ecosyste.ms: Papers

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: podkat

Position-Dependent Kernel Association Test
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: plotGrouper

Shiny app GUI wrapper for ggplot with built-in statistical analysis
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: ClusterJudge

Judging Quality of Clustering Methods using Mutual Information
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: TTMap

Two-Tier Mapper: a clustering tool based on topological data analysis
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: CluMSID

Clustering of MS2 Spectra for Metabolite Identification
Papers that mentioned: 1

Very Likely Science (75)

bioconductor: scRecover

scRecover for imputation of single-cell RNA-seq data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: clippda

A package for the clinical proteomic profiling data analysis
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: optimalFlow

optimalFlow
Papers that mentioned: 1

Very Likely Science (75)

bioconductor: seq2pathway

a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data
Papers that mentioned: 1

Very Likely Science (93)

bioconductor: seqCNA

Copy number analysis of high-throughput sequencing cancer data
Papers that mentioned: 1

Very Likely Science (75)

bioconductor: diffUTR

diffUTR: Streamlining differential exon and 3' UTR usage
Papers that mentioned: 1

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bioconductor: SigFuge

SigFuge
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: ChIPsim

Simulation of ChIP-seq experiments
Papers that mentioned: 1

Very Likely Science (85)

bioconductor: dpeak

dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: SigCheck

Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: ChIPanalyser

ChIPanalyser: Predicting Transcription Factor Binding Sites
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: CexoR

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates
Papers that mentioned: 1

Very Likely Science (98)

bioconductor: dualKS

Papers that mentioned: 1

Unlikely Science (0)

bioconductor: CellTrails

Reconstruction, visualization and analysis of branching trajectories
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: periodicDNA

Set of tools to identify periodic occurrences of k-mers in DNA sequences
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: MAGAR

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: diffloop

Papers that mentioned: 1

Unlikely Science (0)

bioconductor: CancerInSilico

An R interface for computational modeling of tumor progression
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: cancerclass

Development and validation of diagnostic tests from high-dimensional molecular data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: eisaR

Exon-Intron Split Analysis (EISA) in R
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: BUMHMM

Computational pipeline for computing probability of modification from structure probing experiment data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: MSGFgui

Papers that mentioned: 1

Unlikely Science (0)

bioconductor: BasicSTARRseq

Basic peak calling on STARR-seq data
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: SimFFPE

NGS Read Simulator for FFPE Tissue
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: HPAStainR

Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: slalom

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: BLMA

BLMA: A package for bi-level meta-analysis
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: epiNEM

epiNEM
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: VariantFiltering

Filtering of coding and non-coding genetic variants
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: biomvRCNS

Copy Number study and Segmentation for multivariate biological data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: CellScore

Tool for Evaluation of Cell Identity from Transcription Profiles
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: paircompviz

Multiple comparison test visualization
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: CNVRanger

Summarization and expression/phenotype association of CNV ranges
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: biocGraph

Graph examples and use cases in Bioinformatics
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: BicARE

Biclustering Analysis and Results Exploration
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: OTUbase

Provides structure and functions for the analysis of OTU data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: ComPrAn

Complexome Profiling Analysis package
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: FastqCleaner

A Shiny Application for Quality Control, Filtering and Trimming of FASTQ Files
Papers that mentioned: 1

Very Likely Science (75)

bioconductor: fCCAC

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: fcScan

fcScan for detecting clusters of coordinates with user defined options
Papers that mentioned: 1

Very Likely Science (83)

bioconductor: widgetTools

Creates an interactive tcltk widget
Papers that mentioned: 1

Very Likely Science (83)

bioconductor: QuartPAC

Identification of mutational clusters in protein quaternary structures.
Papers that mentioned: 1

Very Likely Science (98)

bioconductor: OpenStats

A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association
Papers that mentioned: 1

Very Likely Science (83)

bioconductor: yamss

Tools for high-throughput metabolomics
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: scDataviz

scDataviz: single cell dataviz and downstream analyses
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: LinkHD

LinkHD: a versatile framework to explore and integrate heterogeneous data
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: openPrimeR

Multiplex PCR Primer Design and Analysis
Papers that mentioned: 1

Very Likely Science (85)

bioconductor: fishpond

Fishpond: downstream methods and tools for expression data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: FilterFFPE

FFPE Artificial Chimeric Read Filter for NGS data
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: onlineFDR

Online error rate control
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: flowcatchR

Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
Papers that mentioned: 1

Very Likely Science (82)

bioconductor: epihet

Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: bgx

Bayesian Gene eXpression
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: BGmix

Bayesian models for differential gene expression
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: chromDraw

chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.
Papers that mentioned: 1

Likely Science (50)

bioconductor: ODER

Optimising the Definition of Expressed Regions
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: geneAttribution

Identification of candidate genes associated with genetic variation
Papers that mentioned: 1

Very Likely Science (85)

bioconductor: srnadiff

Finding differentially expressed unannotated genomic regions from RNA-seq data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: FoldGO

Package for Fold-specific GO Terms Recognition
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: fastLiquidAssociation

functions for genome-wide application of Liquid Association
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: FRGEpistasis

Epistasis Analysis for Quantitative Traits by Functional Regression Model
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: FunChIP

Clustering and Alignment of ChIP-Seq peaks based on their shapes
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: mAPKL

A Hybrid Feature Selection method for gene expression data
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: GAPGOM

GAPGOM (novel Gene Annotation Prediction and other GO Metrics)
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: GeneAccord

Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: pvac

PCA-based gene filtering for Affymetrix arrays
Papers that mentioned: 1

Very Likely Science (98)

bioconductor: GeneTonic

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: mia

Microbiome analysis
Papers that mentioned: 1

Very Likely Science (100)

bioconductor: GeneSelectMMD

Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions
Papers that mentioned: 1

Very Likely Science (75)

bioconductor: sscore

S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
Papers that mentioned: 1

Very Likely Science (100)

bioconductor projects 1,374