bioconductor projects | Ecosyste.ms: Papers

bioconductor: StructuralVariantAnnotation

Variant annotations for structural variants
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: multicrispr

Multi-locus multi-purpose Crispr/Cas design
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: ssviz

A small RNA-seq visualizer and analysis toolkit
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: nanotatoR

Next generation structural variant annotation and classification
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining and Visualization
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: OmaDB

R wrapper for the OMA REST API
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: CNORfeeder

Integration of CellNOptR to add missing links
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: ORFik

Open Reading Frames in Genomics
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: SpatialCPie

Cluster analysis of Spatial Transcriptomics data
Papers that mentioned: 2

Very Likely Science (85)

bioconductor: SNPhood

SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: snm

Supervised Normalization of Microarrays
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: sizepower

Sample Size and Power Calculation in Micorarray Studies
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: singleCellTK

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: PepsNMR

Pre-process 1H-NMR FID signals
Papers that mentioned: 2

Very Likely Science (94)

bioconductor: RUVnormalize

RUV for normalization of expression array data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: projectR

Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: psygenet2r

psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: RImmPort

RImmPort: Enabling Ready-for-analysis Immunology Research Data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: qpcrNorm

Data-driven normalization strategies for high-throughput qPCR data.
Papers that mentioned: 2

Very Likely Science (73)

bioconductor: rfPred

Assign rfPred functional prediction scores to a missense variants list
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: QSutils

Quasispecies Diversity
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: AllelicImbalance

Investigates Allele Specific Expression
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: alpine

alpine
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: ANCOMBC

Microbiome differential abudance and correlation analyses with bias correction
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: rCGH

Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: recount3

Explore and download data from the recount3 project
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: regionReport

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: pathVar

Methods to Find Pathways with Significantly Different Variability
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: omicRexposome

Exposome and omic data associatin and integration analysis
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: RNAAgeCalc

A multi-tissue transcriptional age calculator
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: rnaseqcomp

Benchmarks for RNA-seq Quantification Pipelines
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: BeadDataPackR

Compression of Illumina BeadArray data
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: BiocFileCache

Manage Files Across Sessions
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: BiocOncoTK

Bioconductor components for general cancer genomics
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: BiocSingular

Singular Value Decomposition for Bioconductor Packages
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: rrvgo

Reduce + Visualize GO
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: multiClust

multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: MMUPHin

Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: BPRMeth

Model higher-order methylation profiles
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: MiPP

Misclassification Penalized Posterior Classification
Papers that mentioned: 2

Very Likely Science (98)

bioconductor: Rtreemix

Rtreemix: Mutagenetic trees mixture models.
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: runibic

runibic: row-based biclustering algorithm for analysis of gene expression data in R
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: RUVcorr

Removal of unwanted variation for gene-gene correlations and related analysis
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: rWikiPathways

rWikiPathways - R client library for the WikiPathways API
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: CGHbase

CGHbase: Base functions and classes for arrayCGH data analysis.
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: maskBAD

Masking probes with binding affinity differences
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: maigesPack

Functions to handle cDNA microarray data, including several methods of data analysis
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: chipenrich

Gene Set Enrichment For ChIP-seq Peak Data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: cleaver

Cleavage of Polypeptide Sequences
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: LowMACA

LowMACA - Low frequency Mutation Analysis via Consensus Alignment
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: cicero

Predict cis-co-accessibility from single-cell chromatin accessibility data
Papers that mentioned: 2

Very Likely Science (73)

bioconductor: chromswitch

An R package to detect chromatin state switches from epigenomic data
Papers that mentioned: 2

Very Likely Science (77)

bioconductor: circRNAprofiler

circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: CiteFuse

CiteFuse: multi-modal analysis of CITE-seq data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: cleanUpdTSeq

cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
Papers that mentioned: 2

Very Likely Science (98)

bioconductor: clustComp

Clustering Comparison Package
Papers that mentioned: 2

Very Likely Science (98)

bioconductor: scGPS

A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: KCsmart

Multi sample aCGH analysis package using kernel convolution
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: IONiseR

Quality Assessment Tools for Oxford Nanopore MinION data
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: scReClassify

scReClassify: post hoc cell type classification of single-cell RNA-seq data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: SDAMS

Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: IntEREst

Intron-Exon Retention Estimator
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: clustifyr

Classifier for Single-cell RNA-seq Using Cell Clusters
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: InTAD

Search for correlation between epigenetic signals and gene expression in TADs
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: INPower

An R package for computing the number of susceptibility SNPs
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: SeqSQC

A bioconductor package for sample quality check with next generation sequencing data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: contiBAIT

Improves Early Build Genome Assemblies using Strand-Seq Data
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: sesame

SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: gmapR

An R interface to the GMAP/GSNAP/GSTRUCT suite
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: debrowser

Interactive Differential Expresion Analysis Browser
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: geNetClassifier

Classify diseases and build associated gene networks using gene expression profiles
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: geneplast

Evolutionary and plasticity analysis of orthologous groups
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: genbankr

Parsing GenBank files into semantically useful objects
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: MinimumDistance

A Package for De Novo CNV Detection in Case-Parent Trios
Papers that mentioned: 2

Very Likely Science (73)

bioconductor: gCrisprTools

Suite of Functions for Pooled Crispr Screen QC and Analysis
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: spatialDE

R wrapper for SpatialDE
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: mfa

Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: Risa

Converting experimental metadata from ISA-tab into Bioconductor data structures
Papers that mentioned: 2

Very Likely Science (85)

bioconductor: structToolbox

Data processing & analysis tools for Metabolomics and other omics
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: swfdr

Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: specL

specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: TBSignatureProfiler

Profile RNA-Seq Data Using TB Pathway Signatures
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: tigre

Transcription factor Inference through Gaussian process Reconstruction of Expression
Papers that mentioned: 2

Very Likely Science (95)

bioconductor: ASAFE

Ancestry Specific Allele Frequency Estimation
Papers that mentioned: 2

Very Likely Science (98)

bioconductor: mbkmeans

Mini-batch K-means Clustering for Single-Cell RNA-seq
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: chimeraviz

Visualization tools for gene fusions
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: topconfects

Top Confident Effect Sizes
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: decompTumor2Sig

Decomposition of individual tumors into mutational signatures by signature refitting
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: dagLogo

dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory
Papers that mentioned: 2

Very Likely Science (98)

bioconductor: transcriptogramer

Transcriptional analysis based on transcriptograms
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: Travel

An utility to create an ALTREP object with a virtual pointer
Papers that mentioned: 2

Likely Science (52)

bioconductor: cycle

Significance of periodic expression pattern in time-series data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: CNORfuzzy

Addon to CellNOptR: Fuzzy Logic
Papers that mentioned: 2

Very Likely Science (98)

bioconductor: DiscoRhythm

Interactive Workflow for Discovering Rhythmicity in Biological Data
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: TRONCO

TRONCO, an R package for TRanslational ONCOlogy
Papers that mentioned: 2

Very Likely Science (90)

bioconductor: diffcoexp

Differential Co-expression Analysis
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: CeTF

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: universalmotif

Import, Modify, and Export Motifs with R
Papers that mentioned: 2

Very Likely Science (75)

bioconductor: ExploreModelMatrix

Graphical Exploration of Design Matrices
Papers that mentioned: 2

Very Likely Science (100)

bioconductor: BloodGen3Module

This R package for performing module repertoire analyses and generating fingerprint representations
Papers that mentioned: 2

Very Likely Science (65)

bioconductor projects 1,374