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: ABAEnrichment
Papers that mentioned: 2bioconductor: ABarray
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.Papers that mentioned: 4
bioconductor: ABSSeq
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differencesPapers that mentioned: 7
bioconductor: ACE
Absolute Copy Number Estimation from Low-coverage Whole Genome SequencingPapers that mentioned: 478
bioconductor: aCGH
Classes and functions for Array Comparative Genomic Hybridization dataPapers that mentioned: 32
bioconductor: ACME
Algorithms for Calculating Microarray Enrichment (ACME)Papers that mentioned: 63
bioconductor: affycomp
Graphics Toolbox for Assessment of Affymetrix Expression MeasuresPapers that mentioned: 13
bioconductor: affycoretools
Functions useful for those doing repetitive analyses with Affymetrix GeneChipsPapers that mentioned: 36
bioconductor: affyILM
Linear Model of background subtraction and the Langmuir isothermPapers that mentioned: 2
bioconductor: affyPara
Papers that mentioned: 2bioconductor: AffyRNADegradation
Analyze and correct probe positional bias in microarray data due to RNA degradationPapers that mentioned: 6
bioconductor: AgiMicroRna
Processing and Differential Expression Analysis of Agilent microRNA chipsPapers that mentioned: 37
bioconductor: AIMS
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular SubtypePapers that mentioned: 77
bioconductor: ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountPapers that mentioned: 136
bioconductor: AlphaBeta
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plantsPapers that mentioned: 7
bioconductor: ALPS
Papers that mentioned: 18bioconductor: alsace
Papers that mentioned: 1bioconductor: altcdfenvs
alternative CDF environments (aka probeset mappings)Papers that mentioned: 5
bioconductor: AMARETTO
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized RegressionPapers that mentioned: 5
bioconductor: ANCOMBC
Microbiome differential abudance and correlation analyses with bias correctionPapers that mentioned: 2
bioconductor: AneuFinder
Analysis of Copy Number Variation in Single-Cell-Sequencing DataPapers that mentioned: 16
bioconductor: annmap
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.Papers that mentioned: 5
bioconductor: AnnotationDbi
Manipulation of SQLite-based annotations in BioconductorPapers that mentioned: 73
bioconductor: AnnotationFilter
Facilities for Filtering Bioconductor Annotation ResourcesPapers that mentioned: 1
bioconductor: AnnotationForge
Tools for building SQLite-based annotation data packagesPapers that mentioned: 11
bioconductor: annotationTools
Annotate microarrays and perform cross-species gene expression analyses using flat file databasesPapers that mentioned: 3
bioconductor: annotatr
Annotation of Genomic Regions to Genomic AnnotationsPapers that mentioned: 15
bioconductor: anota2seq
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seqPapers that mentioned: 8
bioconductor: apComplex
Estimate protein complex membership using AP-MS protein dataPapers that mentioned: 2
bioconductor: apeglm
Approximate posterior estimation for GLM coefficientsPapers that mentioned: 41
bioconductor: aroma.light
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data TypesPapers that mentioned: 4
bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSetPapers that mentioned: 1,962
bioconductor: ArrayExpressHTS
ArrayExpress High Throughput Sequencing Processing PipelinePapers that mentioned: 7
bioconductor: arrayMvout
multivariate outlier detection for expression array QAPapers that mentioned: 3
bioconductor: arrayQualityMetrics
Quality metrics report for microarray data setsPapers that mentioned: 190
bioconductor: ARRmNormalization
Adaptive Robust Regression normalization for Illumina methylation dataPapers that mentioned: 1
bioconductor: ASICS
Automatic Statistical Identification in Complex SpectraPapers that mentioned: 10
bioconductor: ASSET
An R package for subset-based association analysis of heterogeneous traits and subtypesPapers that mentioned: 72
bioconductor: ASSIGN
Adaptive Signature Selection and InteGratioN (ASSIGN)Papers that mentioned: 54
bioconductor: attract
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor LandscapePapers that mentioned: 1
bioconductor: AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Papers that mentioned: 45
bioconductor: autonomics
Generifying and intuifying cross-platform omics analysisPapers that mentioned: 6
bioconductor: BaalChIP
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomesPapers that mentioned: 1
bioconductor: BAC
Papers that mentioned: 14bioconductor: bacon
Controlling bias and inflation in association studies using the empirical null distributionPapers that mentioned: 4
bioconductor: BADER
Bayesian Analysis of Differential Expression in RNA Sequencing DataPapers that mentioned: 4
bioconductor: ballgown
Flexible, isoform-level differential expression analysisPapers that mentioned: 21
bioconductor: baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataPapers that mentioned: 139
bioconductor: BBCAnalyzer
BBCAnalyzer: an R/Bioconductor package for visualizing base countsPapers that mentioned: 1
bioconductor: BCRANK
Predicting binding site consensus from ranked DNA sequencesPapers that mentioned: 6
bioconductor: beadarray
Quality assessment and low-level analysis for Illumina BeadArray dataPapers that mentioned: 94
bioconductor: beadarraySNP
Normalization and reporting of Illumina SNP bead arraysPapers that mentioned: 3
bioconductor: BEARscc
BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)Papers that mentioned: 2
bioconductor: BgeeDB
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontologyPapers that mentioned: 4
bioconductor: BiGGR
Constraint based modeling in R using metabolic reconstruction databasesPapers that mentioned: 4
bioconductor: bigmelon
Illumina methylation array analysis for large experimentsPapers that mentioned: 7
bioconductor: bioassayR
Cross-target analysis of small molecule bioactivityPapers that mentioned: 1