Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
bioconductor projects 1,374
bioconductor: msPurity
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in MetabolomicsPapers that mentioned: 2
bioconductor: nanotatoR
Next generation structural variant annotation and classificationPapers that mentioned: 2
bioconductor: NoRCE
NoRCE: Noncoding RNA Sets Cis Annotation and EnrichmentPapers that mentioned: 2
bioconductor: ggtreeExtra
An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"Papers that mentioned: 2
bioconductor: GenoGAM
Papers that mentioned: 2bioconductor: GenomicScores
Infrastructure to work with genomewide position-specific scoresPapers that mentioned: 2
bioconductor: icetea
Integrating Cap Enrichment with Transcript Expression AnalysisPapers that mentioned: 2
bioconductor: HiLDA
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocationPapers that mentioned: 2
bioconductor: loci2path
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLsPapers that mentioned: 2
bioconductor: projectR
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clusteringPapers that mentioned: 2
bioconductor: rCGH
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH DataPapers that mentioned: 2
bioconductor: regionReport
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR resultsPapers that mentioned: 2
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
bioconductor: runibic
runibic: row-based biclustering algorithm for analysis of gene expression data in RPapers that mentioned: 2
bioconductor: rWikiPathways
rWikiPathways - R client library for the WikiPathways APIPapers that mentioned: 2
bioconductor: scMAGeCK
Papers that mentioned: 2bioconductor: scp
Mass Spectrometry-Based Single-Cell Proteomics Data AnalysisPapers that mentioned: 2
bioconductor: scReClassify
scReClassify: post hoc cell type classification of single-cell RNA-seq dataPapers that mentioned: 2
bioconductor: SemDist
Information Accretion-based Function Predictor EvaluationPapers that mentioned: 2
bioconductor: sparseDOSSA
Sparse Data Observations for Simulating Synthetic AbundancePapers that mentioned: 2
bioconductor: SeqSQC
A bioconductor package for sample quality check with next generation sequencing dataPapers that mentioned: 2
bioconductor: sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChipsPapers that mentioned: 2
bioconductor: tigre
Transcription factor Inference through Gaussian process Reconstruction of ExpressionPapers that mentioned: 2
bioconductor: swfdr
Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariatesPapers that mentioned: 2
bioconductor: SwimR
Papers that mentioned: 2bioconductor: TBSignatureProfiler
Profile RNA-Seq Data Using TB Pathway SignaturesPapers that mentioned: 2
bioconductor: Travel
An utility to create an ALTREP object with a virtual pointerPapers that mentioned: 2
bioconductor: twoddpcr
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting moleculesPapers that mentioned: 2
bioconductor: transcriptogramer
Transcriptional analysis based on transcriptogramsPapers that mentioned: 2
bioconductor: TSRchitect
Papers that mentioned: 2bioconductor: structToolbox
Data processing & analysis tools for Metabolomics and other omicsPapers that mentioned: 2
bioconductor: affyILM
Linear Model of background subtraction and the Langmuir isothermPapers that mentioned: 2
bioconductor: apComplex
Estimate protein complex membership using AP-MS protein dataPapers that mentioned: 2
bioconductor: BEARscc
BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)Papers that mentioned: 2
bioconductor: BiocOncoTK
Bioconductor components for general cancer genomicsPapers that mentioned: 2
bioconductor: BiocWorkflowTools
Tools to aid the development of Bioconductor Workflow packagesPapers that mentioned: 2
bioconductor: BloodGen3Module
This R package for performing module repertoire analyses and generating fingerprint representationsPapers that mentioned: 2
bioconductor: CeTF
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysisPapers that mentioned: 2
bioconductor: CGEN
An R package for analysis of case-control studies in genetic epidemiologyPapers that mentioned: 2
bioconductor: cicero
Predict cis-co-accessibility from single-cell chromatin accessibility dataPapers that mentioned: 2
bioconductor: cleanUpdTSeq
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending dataPapers that mentioned: 2
bioconductor: contiBAIT
Improves Early Build Genome Assemblies using Strand-Seq DataPapers that mentioned: 2
bioconductor: cycle
Significance of periodic expression pattern in time-series dataPapers that mentioned: 2
bioconductor: dagLogo
dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theoryPapers that mentioned: 2
bioconductor: decompTumor2Sig
Decomposition of individual tumors into mutational signatures by signature refittingPapers that mentioned: 2
bioconductor: DepecheR
Determination of essential phenotypic elements of clusters in high-dimensional entitiesPapers that mentioned: 2
bioconductor: eudysbiome
Cartesian plot and contingency test on 16S Microbial dataPapers that mentioned: 2
bioconductor: ffpe
Quality assessment and control for FFPE microarray expression dataPapers that mentioned: 2
bioconductor: flowAI
Automatic and interactive quality control for flow cytometry dataPapers that mentioned: 2
bioconductor: flowCut
Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence AnalysisPapers that mentioned: 2
bioconductor: gaga
GaGa hierarchical model for high-throughput data analysisPapers that mentioned: 2
bioconductor: gCrisprTools
Suite of Functions for Pooled Crispr Screen QC and AnalysisPapers that mentioned: 2
bioconductor: genbankr
Parsing GenBank files into semantically useful objectsPapers that mentioned: 2
bioconductor: geneplast
Evolutionary and plasticity analysis of orthologous groupsPapers that mentioned: 2
bioconductor: geNetClassifier
Classify diseases and build associated gene networks using gene expression profilesPapers that mentioned: 2
bioconductor: goSTAG
A tool to use GO Subtrees to Tag and Annotate Genes within a setPapers that mentioned: 2
bioconductor: GreyListChIP
Grey Lists -- Mask Artefact Regions Based on ChIP InputsPapers that mentioned: 2