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: OTUbase
Provides structure and functions for the analysis of OTU dataPapers that mentioned: 1
bioconductor: covEB
Empirical Bayes estimate of block diagonal covariance matricesPapers that mentioned: 1
bioconductor: ClusterJudge
Judging Quality of Clustering Methods using Mutual InformationPapers that mentioned: 1
bioconductor: clippda
A package for the clinical proteomic profiling data analysisPapers that mentioned: 1
bioconductor: CluMSID
Clustering of MS2 Spectra for Metabolite IdentificationPapers that mentioned: 1
bioconductor: cisPath
Visualization and management of the protein-protein interaction networks.Papers that mentioned: 1
bioconductor: pcxn
Exploring, analyzing and visualizing functions utilizing the pcxnData packagePapers that mentioned: 1
bioconductor: cellscape
Explores single cell copy number profiles in the context of a single cell treePapers that mentioned: 1
bioconductor: chromDraw
chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.Papers that mentioned: 1
bioconductor: ChIPanalyser
ChIPanalyser: Predicting Transcription Factor Binding SitesPapers that mentioned: 1
bioconductor: CexoR
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicatesPapers that mentioned: 1
bioconductor: Cepo
Cepo for the identification of differentially stable genesPapers that mentioned: 1
bioconductor: CellTrails
Reconstruction, visualization and analysis of branching trajectoriesPapers that mentioned: 1
bioconductor: plethy
R framework for exploration and analysis of respirometry dataPapers that mentioned: 1
bioconductor: CellScore
Tool for Evaluation of Cell Identity from Transcription ProfilesPapers that mentioned: 1
bioconductor: CancerInSilico
An R interface for computational modeling of tumor progressionPapers that mentioned: 1
bioconductor: cancerclass
Development and validation of diagnostic tests from high-dimensional molecular dataPapers that mentioned: 1
bioconductor: BUMHMM
Computational pipeline for computing probability of modification from structure probing experiment dataPapers that mentioned: 1
bioconductor: PoDCall
Positive Droplet Calling for DNA Methylation Droplet Digital PCRPapers that mentioned: 1
bioconductor: powerTCR
Model-Based Comparative Analysis of the TCR RepertoirePapers that mentioned: 1
bioconductor: biovizBase
Basic graphic utilities for visualization of genomic data.Papers that mentioned: 1
bioconductor: prebs
Probe region expression estimation for RNA-seq data for improved microarray comparabilityPapers that mentioned: 1
bioconductor: biomvRCNS
Copy Number study and Segmentation for multivariate biological dataPapers that mentioned: 1
bioconductor: proBAMr
Generating SAM file for PSMs in shotgun proteomics dataPapers that mentioned: 1
bioconductor: BiocVersion
Set the appropriate version of Bioconductor packagesPapers that mentioned: 1
bioconductor: BBCAnalyzer
BBCAnalyzer: an R/Bioconductor package for visualizing base countsPapers that mentioned: 1
bioconductor: BaalChIP
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomesPapers that mentioned: 1
bioconductor: attract
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor LandscapePapers that mentioned: 1
bioconductor: ARRmNormalization
Adaptive Robust Regression normalization for Illumina methylation dataPapers that mentioned: 1
bioconductor: transcriptR
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and QuantificationPapers that mentioned: 1
bioconductor: tRanslatome
Comparison between multiple levels of gene expressionPapers that mentioned: 1
bioconductor: VariantFiltering
Filtering of coding and non-coding genetic variantsPapers that mentioned: 1
bioconductor: QuartPAC
Identification of mutational clusters in protein quaternary structures.Papers that mentioned: 1
bioconductor: QuaternaryProd
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal GraphsPapers that mentioned: 1
bioconductor: traseR
GWAS trait-associated SNP enrichment analyses in genomic intervalsPapers that mentioned: 1
bioconductor: sRACIPE
Systems biology tool to simulate gene regulatory circuitsPapers that mentioned: 1
bioconductor: signatureSearch
Environment for Gene Expression Searching Combined with Functional Enrichment AnalysisPapers that mentioned: 1
bioconductor: sevenC
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifsPapers that mentioned: 1
bioconductor: similaRpeak
Metrics to estimate a level of similarity between two ChIP-Seq profilesPapers that mentioned: 1
bioconductor: scDataviz
scDataviz: single cell dataviz and downstream analysesPapers that mentioned: 1
bioconductor: scruff
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)Papers that mentioned: 1
bioconductor: scTHI
Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing dataPapers that mentioned: 1
bioconductor: receptLoss
Unsupervised Identification of Genes with Expression Loss in Subsets of TumorsPapers that mentioned: 1
bioconductor: scmeth
Functions to conduct quality control analysis in methylation dataPapers that mentioned: 1
bioconductor: REDseq
Analysis of high-throughput sequencing data processed by restriction enzyme digestionPapers that mentioned: 1
bioconductor: RefPlus
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.Papers that mentioned: 1
bioconductor: SAIGEgds
Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association StudiesPapers that mentioned: 1
bioconductor: segmenter
Perform Chromatin Segmentation Analysis in R by Calling ChromHMMPapers that mentioned: 1
bioconductor: TreeSummarizedExperiment
TreeSummarizedExperiment: a S4 Class for Data with Tree StructuresPapers that mentioned: 1
bioconductor: restfulSE
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interfacePapers that mentioned: 1
bioconductor: RpsiXML
Papers that mentioned: 1bioconductor: BufferedMatrix
A matrix data storage object held in temporary filesPapers that mentioned: 1
bioconductor: RGalaxy
Papers that mentioned: 1bioconductor: rhdf5client
Access HDF5 content from HDF Scalable Data ServicePapers that mentioned: 1
bioconductor: Rhtslib
HTSlib high-throughput sequencing library as an R packagePapers that mentioned: 1
bioconductor: recoup
An R package for the creation of complex genomic profile plotsPapers that mentioned: 1